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/7769667/working' mkdir: created directory `/scratch/stefan/7769667/working/protonate' Storing results in /scratch/stefan/7769667/finished Working in /scratch/stefan/7769667/working /scratch/stefan/7769667/working /scratch/stefan/7769667 /scratch/stefan/7769667/working/protonate /scratch/stefan/7769667/working /scratch/stefan/7769667 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) awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: `/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 Nov 27, 2019 6:16:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:14 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:14 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:14 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:31 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:31 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:31 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:17:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:19 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:19 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:19 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:21 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:21 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:21 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:21 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:36 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:36 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:36 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:38 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:38 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:38 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:43 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:43 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:43 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:43 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:43 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:43 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:18:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:06 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:06 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:06 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:06 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:07 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:07 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:07 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:07 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:07 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:07 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:07 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:07 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:07 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:07 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:09 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:09 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:09 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:12 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:12 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:12 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:12 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:13 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:13 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:13 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:17 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:17 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:17 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:17 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:23 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:23 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:23 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:23 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:24 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:24 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:24 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:24 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:31 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:31 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:31 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:32 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:32 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:32 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:47 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:47 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:47 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:47 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. ph 7.4: 1065 protomers created Coalesing and merging protomers 1032 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1041 protomers after new stereo-center expansion /scratch/stefan/7769667/working /scratch/stefan/7769667 Bulk generating 3D conformations all protomers in /scratch/stefan/7769667/working/3D mkdir: created directory `/scratch/stefan/7769667/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7769667/working/protonate/xaaaadi-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' 1042 3D conformations generated for 1000 compounds Building REAL300000086001 mkdir: created directory `/scratch/stefan/7769667/working/building' mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086001' /scratch/stefan/7769667/working/building/REAL300000086001 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086001 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086001/0 /scratch/stefan/7769667/working/building/REAL300000086001 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1 `/scratch/stefan/7769667/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(COC)C1=CC=CC(Cl)=C1F)C(=O)[O-]) `REAL300000086001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086001 none CCC(NN=C(COC)C1=CC=CC(Cl)=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', '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, 5, 8, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 16, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [128, 86, 40, 10, 10, 1, 10, 31, 59, 1, 1, 1, 1, 1, 1, 1, 1, 86, 114, 114, 128, 128, 128, 128, 128, 86, 40, 31, 31, 59, 59, 59, 1, 1, 1] 170 rigid atoms, others: [32, 33, 34, 5, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 776 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086001 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086001 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `/scratch/stefan/7769667/finished' Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086001/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086001 Building REAL300000086002 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086002' /scratch/stefan/7769667/working/building/REAL300000086002 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086002 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086002/0 /scratch/stefan/7769667/working/building/REAL300000086002 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/2 `/scratch/stefan/7769667/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1COC2=CC(Br)=C(F)C=C21)C(=O)[O-]) `REAL300000086002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086002 none CCC(NN=C1COC2=CC(Br)=C(F)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', '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, 5, 5, 8, 8, 1, 5, 12, 1, 1, 1, 17, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 15, 15, 20, 20, 20, 20, 20, 12, 5, 1, 1, 1, 1] 20 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29] set([0, 1, 2, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086002 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086002 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086002/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086002 Building REAL300000086003 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086003' /scratch/stefan/7769667/working/building/REAL300000086003 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086003 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086003/0 /scratch/stefan/7769667/working/building/REAL300000086003 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/3 `/scratch/stefan/7769667/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCCSC2=CC=C(OC)C=C21)C(=O)[O-]) `REAL300000086003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086003 none CCC(NN=C1CCCSC2=CC=C(OC)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 5, 5, 14, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 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, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 16, 21, 21, 26, 26, 26, 26, 26, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1] 28 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 39] set([0, 1, 2, 36, 37, 38, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086003 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086003 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086003/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086003 Building REAL300000086004 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086004' /scratch/stefan/7769667/working/building/REAL300000086004 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086004 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086004/0 /scratch/stefan/7769667/working/building/REAL300000086004 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/4 `/scratch/stefan/7769667/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)CC1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300000086004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086004 none CCC(NN=C(C)CC1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 15, 14, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 22, 22, 22, 22, 22, 15, 14, 8, 8, 8, 3, 3, 1, 1, 1, 1] 22 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 94 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086004 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086004 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086004/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086004 Building REAL300000086005 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086005' /scratch/stefan/7769667/working/building/REAL300000086005 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086005 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086005/0 /scratch/stefan/7769667/working/building/REAL300000086005 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/5 `/scratch/stefan/7769667/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(OCCCC(=O)[O-])C(OC)=C1)C(=O)[O-]) `REAL300000086005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086005 none CCC(NN=C(C)C1=CC=C(OCCCC(=O)[O-])C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7] 0 hydrogens 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, 32, 20, 9, 9, 1, 9, 1, 1, 1, 1, 1, 10, 29, 35, 48, 60, 60, 1, 1, 3, 1, 32, 37, 37, 37, 37, 37, 37, 37, 32, 20, 9, 9, 9, 1, 1, 29, 29, 35, 35, 48, 48, 3, 3, 3, 1] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 46, 18, 19, 21] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 20, 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: 423 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086005 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086005 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086005/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086005 Building REAL300000086006 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086006' /scratch/stefan/7769667/working/building/REAL300000086006 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086006 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086006/0 /scratch/stefan/7769667/working/building/REAL300000086006 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/6 `/scratch/stefan/7769667/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC(CC)C(=O)[O-])C1=CC=CC=C1OCC(=O)N(C)C) `REAL300000086006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086006 none CCC(=NNC(CC)C(=O)[O-])C1=CC=CC=C1OCC(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 1, 7, 7, 24, 47, 71, 47, 67, 67, 1, 1, 1, 1, 1, 1, 1, 7, 29, 48, 48, 48, 48, 13, 13, 13, 13, 13, 24, 47, 71, 71, 71, 71, 71, 1, 1, 1, 1, 29, 29, 48, 48, 48, 48, 48, 48] 201 rigid atoms, others: [2, 36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 569 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086006 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086006 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086006/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086006 Building REAL300000086007 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086007' /scratch/stefan/7769667/working/building/REAL300000086007 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086007 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086007/0 /scratch/stefan/7769667/working/building/REAL300000086007 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/7 `/scratch/stefan/7769667/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(Cl)N=C(SC2=CC=CC=C2)S1)C(=O)[O-]) `REAL300000086007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086007 none CCC(NN=CC1=C(Cl)N=C(SC2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', '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, 16, 8, 1, 14, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens 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, 23, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 13, 40, 40, 23, 40, 40, 1, 23, 30, 30, 36, 36, 36, 36, 36, 23, 14, 7, 40, 40, 23, 40, 40] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 18] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086007 none CCC(NN=CC1=C(Cl)N=C(SC2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', '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, 16, 8, 1, 14, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 168, 149, 100, 100, 40, 40, 40, 40, 40, 6, 1, 1, 1, 1, 1, 1, 1, 40, 168, 201, 201, 201, 201, 201, 201, 201, 168, 149, 100, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 845 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086007 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086007 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086007/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086007 Building REAL300000086008 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086008' /scratch/stefan/7769667/working/building/REAL300000086008 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086008 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086008/0 /scratch/stefan/7769667/working/building/REAL300000086008 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/8 `/scratch/stefan/7769667/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CNN=C1C1=CC=CC(OC)=C1)C(=O)[O-]) `REAL300000086008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086008 none CCC(NN=CC1=CNN=C1C1=CC=CC(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [64, 40, 19, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 21, 11, 40, 53, 53, 64, 64, 64, 64, 63, 40, 19, 8, 1, 1, 11, 11, 11, 21, 21, 21, 11] 181 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 360 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086008 none CCC(NN=CC1=CNN=C1C1=CC=CC(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [163, 123, 74, 36, 36, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 2, 1, 123, 147, 147, 163, 163, 163, 163, 163, 123, 74, 36, 11, 11, 1, 1, 1, 2, 2, 2, 1] 181 rigid atoms, others: [32, 33, 34, 38, 10, 11, 12, 13, 14, 15, 16, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 784 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086008 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086008 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086008/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086008 Building REAL300000086009 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086009' /scratch/stefan/7769667/working/building/REAL300000086009 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086009 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086009/0 /scratch/stefan/7769667/working/building/REAL300000086009 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/9 `/scratch/stefan/7769667/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(Cl)N=C(Cl)N1C1=CC=CC=C1)C(=O)[O-]) `REAL300000086009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086009 none CCC(NN=CC1=C(Cl)N=C(Cl)N1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'Cl', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 16, 8, 1, 16, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 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: [50, 40, 28, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 40, 47, 47, 50, 50, 50, 50, 50, 40, 27, 13, 4, 4, 4, 4, 4] 59 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086009 none CCC(NN=CC1=C(Cl)N=C(Cl)N1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'Cl', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 16, 8, 1, 16, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 56, 45, 26, 26, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 56, 59, 59, 59, 59, 59, 59, 59, 56, 45, 26, 1, 1, 1, 1, 1] 59 rigid atoms, others: [32, 33, 34, 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]) total number of confs: 211 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086009 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086009 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086009/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086009 Building REAL300000086010 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086010' /scratch/stefan/7769667/working/building/REAL300000086010 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086010 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086010/0 /scratch/stefan/7769667/working/building/REAL300000086010 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/10 `/scratch/stefan/7769667/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCN(C(=O)OC(C)(C)C)C1(C)C)C(=O)[O-]) `REAL300000086010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086010 none CCC(NN=C1CCN(C(=O)OC(C)(C)C)C1(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 3, 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, 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: [37, 22, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 16, 16, 16, 1, 1, 1, 22, 33, 33, 37, 37, 37, 37, 37, 22, 6, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2] 74 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086010 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086010 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086010/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086010 Building REAL300000086011 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086011' /scratch/stefan/7769667/working/building/REAL300000086011 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086011 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086011/0 /scratch/stefan/7769667/working/building/REAL300000086011 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/11 `/scratch/stefan/7769667/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(OC2=CC=CC=C2)C=N1)C(=O)[O-]) `REAL300000086011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086011 none CCC(NN=C(C)C1=CC=C(OC2=CC=CC=C2)C=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', '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.ar', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [80, 56, 23, 5, 5, 1, 5, 1, 1, 1, 1, 1, 9, 19, 19, 12, 19, 19, 1, 1, 56, 71, 71, 80, 80, 80, 80, 80, 56, 23, 6, 6, 6, 1, 1, 19, 19, 19, 19, 19, 1] 201 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 40, 18, 19] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 462 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086011 none CCC(NN=C(C)C1=CC=C(OC2=CC=CC=C2)C=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', '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.ar', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [201, 189, 138, 59, 59, 19, 59, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 189, 194, 194, 201, 201, 201, 201, 201, 189, 138, 59, 59, 59, 19, 19, 1, 1, 1, 1, 1, 19] 201 rigid atoms, others: [35, 36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40]) total number of confs: 758 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086011 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086011 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086011/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086011 Building REAL300000086012 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086012' /scratch/stefan/7769667/working/building/REAL300000086012 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086012 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086012/0 /scratch/stefan/7769667/working/building/REAL300000086012 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/12 `/scratch/stefan/7769667/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CCC(=O)OC(C)(C)C)CC1=CC=CC=C1)C(=O)[O-]) `REAL300000086012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086012 none CCC(NN=C(CCC(=O)OC(C)(C)C)CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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, 5, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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, 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: [23, 17, 13, 8, 8, 3, 8, 12, 12, 26, 26, 31, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 17, 18, 18, 23, 23, 23, 23, 23, 17, 13, 12, 12, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 1, 1, 1, 1, 1] 40 rigid atoms, others: [48, 51, 49, 50, 47, 16, 17, 18, 19, 20, 21, 15] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 188 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086012 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086012 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086012/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086012 Building REAL300000086013 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086013' /scratch/stefan/7769667/working/building/REAL300000086013 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086013 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086013/0 /scratch/stefan/7769667/working/building/REAL300000086013 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/13 `/scratch/stefan/7769667/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC(CC)(CC)CNC(=O)OC(C)(C)C)C(=O)[O-]) `REAL300000086013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086013 none CCC(NN=CC(CC)(CC)CNC(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 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, 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, 9, 6, 5, 5, 1, 1, 1, 2, 1, 2, 1, 3, 6, 10, 10, 10, 10, 10, 10, 9, 11, 11, 11, 11, 11, 11, 11, 9, 6, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10] 31 rigid atoms, others: [9, 11, 5, 6, 7] set([0, 1, 2, 3, 4, 8, 10, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 98 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086013 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086013 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086013/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086013 Building REAL300000086014 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086014' /scratch/stefan/7769667/working/building/REAL300000086014 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086014 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086014/0 /scratch/stefan/7769667/working/building/REAL300000086014 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/14 `/scratch/stefan/7769667/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCCC2=C1C=C(Br)S2)C(=O)[O-]) `REAL300000086014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086014 none CCC(NN=C1CCCC2=C1C=C(Br)S2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 17, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 11, 11, 7, 4, 1, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 42 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086014 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086014 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086014/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086014 Building REAL300000086015 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086015' /scratch/stefan/7769667/working/building/REAL300000086015 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086015 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086015/0 /scratch/stefan/7769667/working/building/REAL300000086015 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/15 `/scratch/stefan/7769667/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC(C2=CC=CC=C2)CC1OC)C(=O)[O-]) `REAL300000086015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086015 none CCC(NN=C1CCC(C2=CC=CC=C2)CC1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 11, 11, 7, 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, 4, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [46, 23, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 1, 6, 23, 37, 37, 46, 46, 46, 46, 46, 23, 7, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 6, 6, 6] 69 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 39, 15, 16, 40, 17, 41, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 274 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086015 none CCC(NN=C1CCC(C2=CC=CC=C2)CC1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 11, 11, 7, 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, 4, 7, 7, 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, 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: [67, 42, 17, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 42, 59, 59, 67, 67, 67, 67, 67, 42, 17, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12] 69 rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44]) total number of confs: 368 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086015 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086015 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086015/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086015 Building REAL300000086016 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086016' /scratch/stefan/7769667/working/building/REAL300000086016 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086016 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086016/0 /scratch/stefan/7769667/working/building/REAL300000086016 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/16 `/scratch/stefan/7769667/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(S(=O)(=O)CC(N)=O)C=C1)C(=O)[O-]) `REAL300000086016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086016 none CCC(NN=C(C)C1=CC=C(S(=O)(=O)CC(N)=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 5, 1, 8, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 6, 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: [59, 41, 22, 6, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 19, 58, 58, 1, 1, 41, 57, 57, 59, 59, 59, 59, 59, 41, 22, 6, 6, 6, 1, 1, 19, 19, 58, 58, 1, 1] 201 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 40, 18, 19, 39] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 497 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086016 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086016 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086016/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086016 Building REAL300000086017 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086017' /scratch/stefan/7769667/working/building/REAL300000086017 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086017 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086017/0 /scratch/stefan/7769667/working/building/REAL300000086017 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/17 `/scratch/stefan/7769667/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CC1=CC=CC=C1Cl)C1=COC=C1)C(=O)[O-]) `REAL300000086017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086017 none CCC(NN=C(CC1=CC=CC=C1Cl)C1=COC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7] 0 hydrogens 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, 132, 78, 31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 31, 90, 90, 90, 90, 132, 142, 142, 147, 147, 147, 147, 147, 132, 78, 6, 6, 1, 1, 1, 1, 90, 90, 90] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086017 none CCC(NN=C(CC1=CC=CC=C1Cl)C1=COC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7] 0 hydrogens 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, 37, 20, 8, 8, 1, 8, 48, 90, 90, 60, 90, 90, 90, 1, 1, 1, 1, 1, 37, 48, 48, 52, 52, 52, 52, 52, 37, 20, 48, 48, 90, 90, 76, 90, 1, 1, 1] 201 rigid atoms, others: [35, 36, 5, 14, 15, 16, 17, 18, 37] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 580 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086017 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086017 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086017/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086017 Building REAL300000086018 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086018' /scratch/stefan/7769667/working/building/REAL300000086018 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086018 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086018/0 /scratch/stefan/7769667/working/building/REAL300000086018 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/18 `/scratch/stefan/7769667/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CC1=C(F)C=CC=C1Cl)C1=COC=C1)C(=O)[O-]) `REAL300000086018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086018 none CCC(NN=C(CC1=C(F)C=CC=C1Cl)C1=COC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', '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, 5, 8, 8, 1, 5, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7] 0 hydrogens 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, 130, 65, 28, 28, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 81, 81, 81, 81, 130, 137, 137, 141, 141, 141, 141, 141, 130, 65, 5, 5, 1, 1, 1, 81, 81, 81] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 690 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086018 none CCC(NN=C(CC1=C(F)C=CC=C1Cl)C1=COC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', '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, 5, 8, 8, 1, 5, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7] 0 hydrogens 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, 31, 17, 8, 8, 1, 8, 49, 81, 81, 81, 81, 81, 81, 81, 1, 1, 1, 1, 1, 31, 35, 35, 36, 36, 36, 36, 36, 31, 17, 49, 49, 81, 81, 81, 1, 1, 1] 201 rigid atoms, others: [35, 36, 5, 15, 16, 17, 18, 19, 37] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 376 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086018 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086018 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086018/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086018 Building REAL300000086019 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086019' /scratch/stefan/7769667/working/building/REAL300000086019 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086019 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086019/0 /scratch/stefan/7769667/working/building/REAL300000086019 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/19 `/scratch/stefan/7769667/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CC1=CC=CC=C1Br)C1=COC=C1)C(=O)[O-]) `REAL300000086019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086019 none CCC(NN=C(CC1=CC=CC=C1Br)C1=COC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7] 0 hydrogens 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, 136, 79, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 30, 92, 92, 92, 92, 136, 145, 145, 148, 148, 148, 148, 148, 136, 79, 6, 6, 1, 1, 1, 1, 92, 92, 92] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086019 none CCC(NN=C(CC1=CC=CC=C1Br)C1=COC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7] 0 hydrogens 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, 39, 21, 8, 8, 1, 8, 48, 92, 92, 48, 92, 92, 92, 1, 1, 1, 1, 1, 39, 49, 49, 52, 52, 52, 52, 52, 39, 21, 48, 48, 92, 92, 72, 92, 1, 1, 1] 201 rigid atoms, others: [35, 36, 5, 14, 15, 16, 17, 18, 37] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 627 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086019 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086019 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086019/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086019 Building REAL300000086020 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086020' /scratch/stefan/7769667/working/building/REAL300000086020 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086020 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086020/0 /scratch/stefan/7769667/working/building/REAL300000086020 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/20 `/scratch/stefan/7769667/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CC1=CC=C(F)C=C1Cl)C1=COC=C1)C(=O)[O-]) `REAL300000086020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086020 none CCC(NN=C(CC1=CC=C(F)C=C1Cl)C1=COC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', '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, 5, 8, 8, 1, 5, 1, 1, 1, 1, 15, 1, 1, 16, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [149, 135, 79, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 94, 94, 94, 94, 135, 145, 145, 149, 149, 149, 149, 149, 135, 79, 6, 6, 1, 1, 1, 94, 94, 94] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 734 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086020 none CCC(NN=C(CC1=CC=C(F)C=C1Cl)C1=COC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', '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, 5, 8, 8, 1, 5, 1, 1, 1, 1, 15, 1, 1, 16, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 33, 17, 8, 8, 1, 8, 49, 94, 94, 74, 80, 94, 94, 94, 1, 1, 1, 1, 1, 33, 45, 45, 48, 48, 48, 48, 48, 33, 17, 49, 49, 94, 94, 94, 1, 1, 1] 201 rigid atoms, others: [35, 36, 5, 15, 16, 17, 18, 19, 37] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 546 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086020 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086020 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086020/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086020 Building REAL300000086021 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086021' /scratch/stefan/7769667/working/building/REAL300000086021 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086021 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086021/0 /scratch/stefan/7769667/working/building/REAL300000086021 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/21 `/scratch/stefan/7769667/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCN(C(=O)OC(C)(C)C)C(C2=CC=CC=C2)C1)C(=O)[O-]) `REAL300000086021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086021 none CCC(NN=C1CCN(C(=O)OC(C)(C)C)C(C2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 3, 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, 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: [30, 19, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 15, 1, 1, 2, 2, 1, 2, 2, 1, 19, 26, 26, 30, 30, 30, 30, 30, 19, 8, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 1, 2, 2, 1, 1] 77 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 47, 16, 17, 35, 53, 54, 23, 36, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086021 none CCC(NN=C1CCN(C(=O)OC(C)(C)C)C(C2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 3, 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, 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: [30, 19, 8, 2, 2, 2, 2, 2, 2, 2, 5, 5, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 2, 19, 26, 26, 30, 30, 30, 30, 30, 19, 8, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 2, 2] 77 rigid atoms, others: [48, 51, 49, 50, 16, 17, 18, 19, 20, 21, 22, 52] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 53, 54]) total number of confs: 177 number of broken/clashed sets: 77 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086021 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086021 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086021/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086021 Building REAL300000086022 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086022' /scratch/stefan/7769667/working/building/REAL300000086022 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086022 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086022/0 /scratch/stefan/7769667/working/building/REAL300000086022 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/22 `/scratch/stefan/7769667/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC2=C1C=C(Br)S2)C(=O)[O-]) `REAL300000086022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086022 none CCC(NN=C1CCC2=C1C=C(Br)S2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 17, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 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: [21, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 18, 18, 21, 21, 21, 21, 21, 16, 7, 1, 1, 1, 1, 1] 22 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086022 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086022 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086022/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086022 Building REAL300000086023 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086023' /scratch/stefan/7769667/working/building/REAL300000086023 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086023 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086023/0 /scratch/stefan/7769667/working/building/REAL300000086023 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/23 `/scratch/stefan/7769667/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC(Br)=CC=C1OCC(=O)[O-])C(=O)[O-]) `REAL300000086023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086023 none CCC(NN=C(C)C1=CC(Br)=CC=C1OCC(=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 5, 8, 8, 1, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [51, 31, 20, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 32, 52, 52, 31, 39, 39, 51, 51, 51, 51, 51, 31, 20, 8, 8, 8, 1, 1, 1, 32, 32] 146 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 425 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086023 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086023 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086023/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086023 Building REAL300000086024 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086024' /scratch/stefan/7769667/working/building/REAL300000086024 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086024 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086024/0 /scratch/stefan/7769667/working/building/REAL300000086024 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/24 `/scratch/stefan/7769667/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1)C(=O)[O-]) `REAL300000086024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086024 none CCC(NN=C(C)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1)C(=O)[O-] 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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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, 5, 5, 8, 8, 1, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 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 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 1] 3 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 41, 37] set([0, 1, 2, 3, 4, 6, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 23 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086024 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086024 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086024/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086024 Building REAL300000086025 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086025' /scratch/stefan/7769667/working/building/REAL300000086025 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086025 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086025/0 /scratch/stefan/7769667/working/building/REAL300000086025 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/25 `/scratch/stefan/7769667/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(Cl)N=C2C(=C1)C(C)=NN2C1=CC=CC=C1)C(=O)[O-]) `REAL300000086025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086025 none CCC(NN=CC1=C(Cl)N=C2C(=C1)C(C)=NN2C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 16, 8, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 45, 46, 46, 50, 50, 50, 50, 50, 45, 28, 8, 1, 2, 2, 2, 4, 4, 2, 4, 4] 50 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 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: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086025 none CCC(NN=CC1=C(Cl)N=C2C(=C1)C(C)=NN2C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 16, 8, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 34, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 50, 50, 49, 34, 15, 4, 4, 4, 4, 1, 1, 1, 1, 1] 50 rigid atoms, others: [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, 35, 36, 37]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086025 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086025 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086025/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086025 Building REAL300000086026 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086026' /scratch/stefan/7769667/working/building/REAL300000086026 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086026 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086026/0 /scratch/stefan/7769667/working/building/REAL300000086026 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/26 `/scratch/stefan/7769667/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=CC(C)=C1O)C(=O)[O-]) `REAL300000086026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086026 none CCC(NN=CC1=CC(Br)=CC(C)=C1O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.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, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 5, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 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, 30, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 40, 40, 40, 40, 40, 30, 22, 7, 1, 1, 2, 2, 2, 2] 80 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 158 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086026 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086026 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086026/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086026 Building REAL300000086027 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086027' /scratch/stefan/7769667/working/building/REAL300000086027 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086027 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086027/0 /scratch/stefan/7769667/working/building/REAL300000086027 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/27 `/scratch/stefan/7769667/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(Cl)C=C1N1C=NC=N1)C(=O)[O-]) `REAL300000086027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086027 none CCC(NN=CC1=CC=C(Cl)C=C1N1C=NC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.2', 'O.co2', 'O.co2', '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, 16, 1, 1, 8, 1, 8, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 14, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 15, 15, 20, 20, 20, 20, 20, 14, 11, 6, 1, 1, 1, 5, 5] 20 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086027 none CCC(NN=CC1=CC=C(Cl)C=C1N1C=NC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.2', 'O.co2', 'O.co2', '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, 16, 1, 1, 8, 1, 8, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 14, 12, 8, 8, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 15, 15, 20, 20, 20, 20, 20, 14, 12, 8, 5, 5, 5, 1, 1] 20 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086027 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086027 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086027/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086027 Building REAL300000086028 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086028' /scratch/stefan/7769667/working/building/REAL300000086028 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086028 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086028/0 /scratch/stefan/7769667/working/building/REAL300000086028 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/28 `/scratch/stefan/7769667/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(N2C(=O)CCC2=O)C=C1)C(=O)[O-]) `REAL300000086028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086028 none CCC(NN=C(C)C1=CC=C(N2C(=O)CCC2=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [72, 59, 29, 6, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 59, 66, 66, 72, 72, 72, 72, 72, 59, 29, 6, 6, 6, 1, 1, 6, 6, 6, 6, 1, 1] 88 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 40, 18, 19, 39] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 325 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086028 none CCC(NN=C(C)C1=CC=C(N2C(=O)CCC2=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [87, 73, 44, 10, 11, 1, 11, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 71, 79, 79, 87, 87, 87, 88, 87, 71, 46, 11, 10, 11, 10, 10, 1, 1, 1, 1, 10, 10] 88 rigid atoms, others: [35, 36, 38, 10, 11, 12, 13, 14, 15, 16, 17, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40]) total number of confs: 396 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086028 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086028 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086028/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086028 Building REAL300000086029 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086029' /scratch/stefan/7769667/working/building/REAL300000086029 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086029 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086029/0 /scratch/stefan/7769667/working/building/REAL300000086029 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/29 `/scratch/stefan/7769667/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1(CNC(=O)OC(C)(C)C)CCOCC1)C(=O)[O-]) `REAL300000086029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086029 none CCC(NN=CC1(CNC(=O)OC(C)(C)C)CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 23, 8, 8, 1, 1, 1, 6, 20, 31, 31, 61, 69, 69, 69, 1, 1, 1, 1, 1, 47, 70, 70, 74, 74, 74, 74, 74, 47, 22, 8, 6, 6, 20, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [48, 50, 5, 6, 7, 44, 45, 46, 47, 16, 17, 18, 19, 20, 49, 51] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 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: 632 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086029 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086029 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086029/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086029 Building REAL300000086030 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086030' /scratch/stefan/7769667/working/building/REAL300000086030 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086030 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086030/0 /scratch/stefan/7769667/working/building/REAL300000086030 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/30 `/scratch/stefan/7769667/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=CC(Br)=C1)C(=O)[O-]) `REAL300000086030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086030 none CCC(NN=CC1=CC(Br)=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [42, 27, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 31, 31, 42, 42, 42, 42, 42, 27, 17, 4, 1, 1, 1] 43 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086030 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086030 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086030/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086030 Building REAL300000086031 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086031' /scratch/stefan/7769667/working/building/REAL300000086031 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086031 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086031/0 /scratch/stefan/7769667/working/building/REAL300000086031 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/31 `/scratch/stefan/7769667/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(OC)=C(OCC(F)F)C(OC)=C1)C(=O)[O-]) `REAL300000086031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086031 none CCC(NN=CC1=CC(OC)=C(OCC(F)F)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 12, 5, 1, 12, 5, 5, 15, 15, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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: [34, 24, 14, 6, 6, 1, 1, 1, 1, 1, 3, 1, 1, 2, 14, 45, 45, 1, 1, 3, 1, 24, 25, 25, 34, 34, 34, 34, 34, 24, 14, 6, 1, 4, 4, 4, 14, 14, 45, 4, 4, 4, 1] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 42, 11, 12, 17, 18, 20] set([0, 1, 2, 3, 4, 10, 13, 14, 15, 16, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 348 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086031 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086031 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086031/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086031 Building REAL300000086032 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086032' /scratch/stefan/7769667/working/building/REAL300000086032 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086032 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086032/0 /scratch/stefan/7769667/working/building/REAL300000086032 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/32 `/scratch/stefan/7769667/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CC1CCOC1)C1=CC=C(F)C=C1)C(=O)[O-]) `REAL300000086032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086032 none CCC(NN=C(CC1CCOC1)C1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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] 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: [150, 121, 78, 26, 26, 7, 1, 1, 1, 1, 1, 1, 26, 47, 47, 30, 32, 47, 47, 121, 129, 129, 150, 150, 150, 150, 150, 121, 78, 7, 7, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47] 173 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41]) total number of confs: 709 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086032 none CCC(NN=C(CC1CCOC1)C1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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] 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: [121, 74, 33, 6, 6, 1, 6, 29, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 74, 102, 102, 121, 121, 121, 121, 121, 74, 33, 29, 29, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1] 173 rigid atoms, others: [5, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 792 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086032 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086032 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086032/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086032 Building REAL300000086033 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086033' /scratch/stefan/7769667/working/building/REAL300000086033 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086033 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086033/0 /scratch/stefan/7769667/working/building/REAL300000086033 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/33 `/scratch/stefan/7769667/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(C2=CC=CC=C2Br)N=N1)C(=O)[O-]) `REAL300000086033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086033 none CCC(NN=CC1=CN(C2=CC=CC=C2Br)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 1, 1, 1, 1, 17, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 6, 3, 3, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 4, 1, 1, 12, 12, 12, 14, 14, 14, 14, 14, 12, 6, 3, 1, 4, 4, 2, 4] 20 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086033 none CCC(NN=CC1=CN(C2=CC=CC=C2Br)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 1, 1, 1, 1, 17, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 18, 11, 5, 5, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 18, 18, 18, 20, 20, 20, 20, 20, 18, 11, 5, 4, 1, 1, 1, 1] 20 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086033 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086033 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086033/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086033 Building REAL300000086034 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086034' /scratch/stefan/7769667/working/building/REAL300000086034 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086034 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086034/0 /scratch/stefan/7769667/working/building/REAL300000086034 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/34 `/scratch/stefan/7769667/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C2NC(=O)C(=O)NC2=C1)C(=O)[O-]) `REAL300000086034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086034 none CCC(NN=C(C)C1=CC=C2NC(=O)C(=O)NC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 11, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 75, 46, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 80, 80, 87, 87, 87, 87, 87, 75, 46, 11, 11, 11, 1, 1, 1, 1, 1] 87 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 364 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086034 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086034 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086034/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086034 Building REAL300000086035 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086035' /scratch/stefan/7769667/working/building/REAL300000086035 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086035 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086035/0 /scratch/stefan/7769667/working/building/REAL300000086035 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/35 `/scratch/stefan/7769667/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCCCC1C1CCCN1C(=O)OC(C)(C)C)C(=O)[O-]) `REAL300000086035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086035 none CCC(NN=C1CCCCC1C1CCCN1C(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.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', '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, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 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: [32, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 11, 11, 23, 30, 30, 30, 21, 31, 31, 32, 32, 32, 32, 32, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 30, 30, 30, 30, 30, 30, 30, 30, 30] 89 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 39, 11, 40, 35, 41, 36, 38, 37] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 261 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086035 none CCC(NN=C1CCCCC1C1CCCN1C(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.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', '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, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [42, 31, 13, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 16, 22, 22, 22, 31, 40, 40, 42, 42, 42, 42, 42, 31, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22] 89 rigid atoms, others: [16, 45, 43, 44, 10, 11, 12, 13, 14, 15, 48, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 271 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086035 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086035 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086035/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086035 Building REAL300000086036 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086036' /scratch/stefan/7769667/working/building/REAL300000086036 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086036 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086036/0 /scratch/stefan/7769667/working/building/REAL300000086036 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/36 `/scratch/stefan/7769667/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(I)=CC([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300000086036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086036 none CCC(NN=CC1=CC(I)=CC([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 18, 1, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 59, 38, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 62, 62, 81, 81, 81, 81, 81, 59, 38, 8, 1, 1, 1] 81 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086036 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086036 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086036/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086036 Building REAL300000086037 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086037' /scratch/stefan/7769667/working/building/REAL300000086037 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086037 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086037/0 /scratch/stefan/7769667/working/building/REAL300000086037 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/37 `/scratch/stefan/7769667/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C(=O)N(CC[NH+](C)C)C2=CC=CC=C21)C(=O)[O-]) `REAL300000086037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086037 none CCC(NN=C1C(=O)N(CC[NH+](C)C)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 7, 7, 6, 7, 7, 7, 1, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 8, 8, 10, 10, 10, 10, 10, 7, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 11 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 42, 43, 44, 15, 16, 17, 18, 19, 20, 41] set([0, 1, 2, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 64 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086037 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086037 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086037/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086037 Building REAL300000086038 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086038' /scratch/stefan/7769667/working/building/REAL300000086038 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086038 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086038/0 /scratch/stefan/7769667/working/building/REAL300000086038 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/38 `/scratch/stefan/7769667/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CC1CCCO1)C1=CC=C(F)C=C1)C(=O)[O-]) `REAL300000086038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086038 none CCC(NN=C(CC1CCCO1)C1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [62, 46, 36, 18, 18, 7, 1, 1, 1, 1, 1, 1, 18, 32, 32, 32, 32, 32, 32, 46, 56, 56, 62, 62, 62, 62, 62, 46, 36, 7, 7, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32] 80 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41]) total number of confs: 322 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086038 none CCC(NN=C(CC1CCCO1)C1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [67, 47, 31, 7, 7, 1, 7, 21, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 47, 61, 61, 67, 67, 67, 67, 67, 47, 31, 21, 21, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1] 80 rigid atoms, others: [5, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 429 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086038 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086038 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086038/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086038 Building REAL300000086039 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086039' /scratch/stefan/7769667/working/building/REAL300000086039 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086039 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086039/0 /scratch/stefan/7769667/working/building/REAL300000086039 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/39 `/scratch/stefan/7769667/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(N(C)C)N(C)C(=O)N(C)C1=O)C(=O)[O-]) `REAL300000086039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086039 none CCC(NN=CC1=C(N(C)C)N(C)C(=O)N(C)C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 8, 5, 1, 11, 8, 5, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 25, 21, 9, 9, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 25, 29, 29, 30, 30, 30, 30, 30, 25, 21, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 30 rigid atoms, others: [5, 6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 9, 10, 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: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086039 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086039 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086039/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086039 Building REAL300000086040 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086040' /scratch/stefan/7769667/working/building/REAL300000086040 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086040 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086040/0 /scratch/stefan/7769667/working/building/REAL300000086040 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/40 `/scratch/stefan/7769667/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(Cl)C=C(Cl)C=C1N(C)C)C(=O)[O-]) `REAL300000086040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086040 none CCC(NN=CC1=C(Cl)C=C(Cl)C=C1N(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 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: [42, 34, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 34, 37, 37, 42, 42, 42, 42, 42, 34, 24, 7, 1, 1, 4, 4, 4, 4, 4, 4] 43 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086040 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086040 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086040/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086040 Building REAL300000086041 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086041' /scratch/stefan/7769667/working/building/REAL300000086041 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086041 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086041/0 /scratch/stefan/7769667/working/building/REAL300000086041 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/41 `/scratch/stefan/7769667/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCN(C(=O)OC(C)(C)C)CC1C)C(=O)[O-]) `REAL300000086041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086041 none CCC(NN=C1CCN(C(=O)OC(C)(C)C)CC1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 3, 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, 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: [47, 27, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 23, 23, 23, 1, 1, 1, 27, 40, 40, 47, 47, 47, 47, 47, 27, 8, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 2, 2, 2] 107 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 42, 43, 44, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47]) total number of confs: 319 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086041 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086041 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086041/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086041 Building REAL300000086042 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086042' /scratch/stefan/7769667/working/building/REAL300000086042 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086042 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086042/0 /scratch/stefan/7769667/working/building/REAL300000086042 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/42 `/scratch/stefan/7769667/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C(C)OCC1=CC=CC=C1)C(F)(F)F)C(=O)[O-]) `REAL300000086042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086042 none CCC(NN=C(C(C)OCC1=CC=CC=C1)C(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 5, 5, 8, 8, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 151, 93, 93, 38, 13, 38, 4, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 197, 200, 200, 201, 201, 201, 201, 201, 197, 151, 38, 38, 38, 38, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 798 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086042 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086042 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086042/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086042 Building REAL300000086043 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086043' /scratch/stefan/7769667/working/building/REAL300000086043 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086043 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086043/0 /scratch/stefan/7769667/working/building/REAL300000086043 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/43 `/scratch/stefan/7769667/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(CC(CC2=CC=C(Cl)C=C2)=NNC(CC)C(=O)[O-])N=C1) `REAL300000086043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086043 none CCC1=CC=C(CC(CC2=CC=C(Cl)C=C2)=NNC(CC)C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.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, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 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: [2, 1, 1, 1, 1, 1, 1, 7, 14, 41, 49, 49, 49, 49, 49, 49, 14, 14, 46, 69, 82, 69, 79, 79, 1, 1, 3, 3, 3, 2, 2, 1, 1, 7, 7, 41, 41, 49, 49, 49, 49, 46, 69, 82, 82, 82, 82, 82, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 48, 24, 25, 31] set([0, 7, 8, 9, 10, 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, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 526 number of broken/clashed sets: 110 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086043 none CCC1=CC=C(CC(CC2=CC=C(Cl)C=C2)=NNC(CC)C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.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, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 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: [95, 49, 49, 49, 49, 36, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 30, 40, 44, 40, 43, 43, 49, 49, 95, 95, 95, 95, 95, 49, 49, 36, 36, 4, 4, 1, 1, 1, 1, 30, 40, 44, 44, 44, 44, 44, 49] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 576 number of broken/clashed sets: 110 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086043 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086043 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086043/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086043 Building REAL300000086044 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086044' /scratch/stefan/7769667/working/building/REAL300000086044 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086044 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086044/0 /scratch/stefan/7769667/working/building/REAL300000086044 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/44 `/scratch/stefan/7769667/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)CCCCNC(=O)OC(C)(C)C)C(=O)[O-]) `REAL300000086044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086044 none CCC(NN=C(C)CCCCNC(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 11, 10, 10, 3, 10, 1, 1, 1, 1, 3, 5, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 10, 10, 10, 3, 3, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11] 31 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 95 number of broken/clashed sets: 1 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086044 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086044 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086044/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086044 Building REAL300000086045 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086045' /scratch/stefan/7769667/working/building/REAL300000086045 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086045 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086045/0 /scratch/stefan/7769667/working/building/REAL300000086045 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/45 `/scratch/stefan/7769667/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C(F)(F)F)=CC=C1Br)C(=O)[O-]) `REAL300000086045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086045 none CCC(NN=CC1=CC(C(F)(F)F)=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 39, 27, 9, 9, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 39, 43, 43, 54, 54, 54, 54, 54, 39, 27, 9, 1, 1, 1] 54 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086045 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086045 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086045/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086045 Building REAL300000086046 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086046' /scratch/stefan/7769667/working/building/REAL300000086046 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086046 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086046/0 /scratch/stefan/7769667/working/building/REAL300000086046 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/46 `/scratch/stefan/7769667/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC(C)=CC1=CC=CC=C1OC(F)F)C(=O)[O-]) `REAL300000086046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086046 none CCC(NN=CC(C)=CC1=CC=CC=C1OC(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', '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, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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, 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: [65, 31, 13, 7, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 54, 54, 31, 55, 55, 65, 65, 65, 65, 65, 31, 13, 7, 4, 4, 4, 4, 1, 1, 1, 1, 54] 186 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 562 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086046 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086046 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086046/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086046 Building REAL300000086047 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086047' /scratch/stefan/7769667/working/building/REAL300000086047 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086047 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086047/0 /scratch/stefan/7769667/working/building/REAL300000086047 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/47 `/scratch/stefan/7769667/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Cl)=CC(Cl)=C1[N+](=O)[O-])C(=O)[O-]) `REAL300000086047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086047 none CCC(NN=CC1=CC(Cl)=CC(Cl)=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 46, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 46, 48, 48, 58, 58, 58, 58, 58, 46, 27, 6, 1, 1] 58 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086047 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086047 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086047/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086047 Building REAL300000086048 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086048' /scratch/stefan/7769667/working/building/REAL300000086048 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086048 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086048/0 /scratch/stefan/7769667/working/building/REAL300000086048 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/48 `/scratch/stefan/7769667/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN2C=CC(Br)=CC2=N1)C(=O)[O-]) `REAL300000086048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086048 none CCC(NN=CC1=CN2C=CC(Br)=CC2=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 17, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 28, 16, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 38, 38, 38, 38, 38, 28, 16, 7, 1, 1, 1, 1] 38 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086048 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086048 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086048/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086048 Building REAL300000086049 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086049' /scratch/stefan/7769667/working/building/REAL300000086049 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086049 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086049/0 /scratch/stefan/7769667/working/building/REAL300000086049 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/49 `/scratch/stefan/7769667/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1CCN(C(=O)OC(C)(C)C)CC1C)C(=O)[O-]) `REAL300000086049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086049 none CCC(NN=CC1CCN(C(=O)OC(C)(C)C)CC1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 72, 39, 9, 9, 1, 1, 1, 1, 1, 1, 6, 6, 17, 19, 20, 19, 1, 1, 1, 72, 88, 88, 93, 93, 93, 93, 93, 72, 39, 9, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 45, 46, 47, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 48, 49, 50]) total number of confs: 507 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086049 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086049 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086049/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086049 Building REAL300000086050 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086050' /scratch/stefan/7769667/working/building/REAL300000086050 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086050 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086050/0 /scratch/stefan/7769667/working/building/REAL300000086050 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/50 `/scratch/stefan/7769667/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CCCC1=CC=CC=C1)C1=CC=C(F)C=C1)C(=O)[O-]) `REAL300000086050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086050 none CCC(NN=C(CCCC1=CC=CC=C1)C1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 179, 125, 54, 54, 10, 5, 3, 1, 1, 1, 1, 1, 1, 1, 54, 94, 94, 80, 94, 94, 94, 179, 193, 193, 201, 201, 201, 201, 201, 179, 125, 10, 10, 5, 5, 3, 3, 1, 1, 1, 1, 1, 94, 94, 94, 94] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46]) total number of confs: 976 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086050 none CCC(NN=C(CCCC1=CC=CC=C1)C1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 33, 16, 4, 4, 1, 4, 30, 44, 77, 94, 94, 93, 94, 94, 1, 1, 1, 1, 1, 1, 1, 33, 43, 43, 49, 49, 49, 49, 49, 33, 16, 30, 30, 50, 50, 77, 77, 94, 94, 94, 94, 94, 1, 1, 1, 1] 201 rigid atoms, others: [5, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 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, 38, 39, 40, 41, 42]) total number of confs: 653 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086050 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086050 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086050/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086050 Building REAL300000086051 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086051' /scratch/stefan/7769667/working/building/REAL300000086051 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086051 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086051/0 /scratch/stefan/7769667/working/building/REAL300000086051 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/51 `/scratch/stefan/7769667/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C(=O)OC)=CC=C1[N+](=O)[O-])C(=O)[O-]) `REAL300000086051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086051 none CCC(NN=CC1=CC(C(=O)OC)=CC=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 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, 12, 7, 4, 4, 1, 1, 1, 1, 1, 6, 6, 6, 1, 1, 1, 1, 2, 2, 12, 12, 12, 19, 19, 19, 19, 19, 12, 7, 4, 1, 7, 7, 7, 1, 1] 25 rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086051 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086051 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086051/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086051 Building REAL300000086052 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086052' /scratch/stefan/7769667/working/building/REAL300000086052 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086052 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086052/0 /scratch/stefan/7769667/working/building/REAL300000086052 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/52 `/scratch/stefan/7769667/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(S(N)(=O)=O)C(Cl)=C1)C(=O)[O-]) `REAL300000086052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086052 none CCC(NN=CC1=CC=C(S(N)(=O)=O)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 14, 8, 11, 11, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 47, 29, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 47, 50, 50, 55, 55, 55, 55, 55, 47, 29, 6, 1, 1, 2, 2, 1] 55 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086052 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086052 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086052/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086052 Building REAL300000086053 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086053' /scratch/stefan/7769667/working/building/REAL300000086053 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086053 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086053/0 /scratch/stefan/7769667/working/building/REAL300000086053 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/53 `/scratch/stefan/7769667/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCCC2=CC=C(S(N)(=O)=O)C=C21)C(=O)[O-]) `REAL300000086053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086053 none CCC(NN=C1CCCC2=CC=C(S(N)(=O)=O)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [29, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 18, 26, 26, 29, 29, 29, 29, 29, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1] 60 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 39] set([0, 1, 2, 37, 38, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 174 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086053 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086053 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086053/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086053 Building REAL300000086054 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086054' /scratch/stefan/7769667/working/building/REAL300000086054 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086054 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086054/0 /scratch/stefan/7769667/working/building/REAL300000086054 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/54 `/scratch/stefan/7769667/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1[C@@H]2CCC[C@H]1CC1=CC=CC=C1C2)C(=O)[O-]) `REAL300000086054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086054 none CCC(NN=C1[C@@H]2CCC[C@H]1CC1=CC=CC=C1C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 7, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 18, 18, 18, 18, 18, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 18 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 66 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086054 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086054 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086054/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086054 Building REAL300000086055 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086055' /scratch/stefan/7769667/working/building/REAL300000086055 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086055 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086055/0 /scratch/stefan/7769667/working/building/REAL300000086055 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/55 `/scratch/stefan/7769667/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(C2=C(F)C=CC=C2F)C=C1)C(=O)[O-]) `REAL300000086055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086055 none CCC(NN=C(C)C1=CC=C(C2=C(F)C=CC=C2F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 1, 1, 15, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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] 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: [72, 58, 30, 6, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 1, 1, 58, 65, 65, 72, 72, 72, 72, 72, 58, 30, 7, 7, 7, 1, 1, 6, 1, 6, 1, 1] 83 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 40, 19, 20, 39] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 333 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086055 none CCC(NN=C(C)C1=CC=C(C2=C(F)C=CC=C2F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 1, 1, 15, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 76, 55, 15, 13, 1, 13, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 77, 83, 83, 83, 83, 82, 83, 83, 75, 55, 14, 15, 15, 10, 10, 1, 1, 1, 10, 10] 83 rigid atoms, others: [36, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 346 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086055 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086055 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086055/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086055 Building REAL300000086056 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086056' /scratch/stefan/7769667/working/building/REAL300000086056 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086056 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086056/0 /scratch/stefan/7769667/working/building/REAL300000086056 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/56 `/scratch/stefan/7769667/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CNC2=CC=C(C(C)(C)C)C=C12)C(=O)[O-]) `REAL300000086056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086056 none CCC(NN=CC1=CNC2=CC=C(C(C)(C)C)C=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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, 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: [78, 65, 41, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 65, 69, 69, 78, 78, 78, 78, 78, 65, 41, 10, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1] 137 rigid atoms, others: [32, 33, 43, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086056 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086056 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086056/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086056 Building REAL300000086057 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086057' /scratch/stefan/7769667/working/building/REAL300000086057 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086057 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086057/0 /scratch/stefan/7769667/working/building/REAL300000086057 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/57 `/scratch/stefan/7769667/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(Br)C=C(C)S1)C(=O)[O-]) `REAL300000086057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086057 none CCC(NN=CC1=C(Br)C=C(C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 17, 1, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 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: [68, 51, 36, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 51, 54, 54, 68, 68, 68, 68, 68, 51, 35, 11, 1, 2, 2, 2] 69 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 24] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086057 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086057 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086057/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086057 Building REAL300000086058 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086058' /scratch/stefan/7769667/working/building/REAL300000086058 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086058 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086058/0 /scratch/stefan/7769667/working/building/REAL300000086058 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/58 `/scratch/stefan/7769667/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCCC(C2=CC=CC(Cl)=C2)C1)C(=O)[O-]) `REAL300000086058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086058 none CCC(NN=C1CCCC(C2=CC=CC(Cl)=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 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: [29, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 13, 13, 1, 22, 27, 27, 29, 29, 29, 29, 29, 22, 7, 1, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 1, 1] 98 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 39, 17, 40, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 156 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086058 none CCC(NN=C1CCCC(C2=CC=CC(Cl)=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [98, 82, 52, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 82, 90, 90, 98, 98, 98, 98, 98, 82, 52, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13] 98 rigid atoms, others: [35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40]) total number of confs: 406 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086058 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086058 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086058/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086058 Building REAL300000086059 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086059' /scratch/stefan/7769667/working/building/REAL300000086059 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086059 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086059/0 /scratch/stefan/7769667/working/building/REAL300000086059 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/59 `/scratch/stefan/7769667/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C(NC(C)=O)C1=CC=CC=C1F)C(=O)[O-]) `REAL300000086059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086059 none CCC(NN=C(C)C(NC(C)=O)C1=CC=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 5, 8, 1, 5, 11, 1, 1, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 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, 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: [123, 101, 79, 28, 28, 11, 28, 1, 11, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 101, 113, 113, 123, 123, 123, 123, 123, 101, 79, 28, 28, 28, 11, 16, 16, 16, 16, 1, 1, 1, 1] 138 rigid atoms, others: [37, 38, 7, 40, 39, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 541 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086059 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086059 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086059/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086059 Building REAL300000086060 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086060' /scratch/stefan/7769667/working/building/REAL300000086060 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086060 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086060/0 /scratch/stefan/7769667/working/building/REAL300000086060 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/60 `/scratch/stefan/7769667/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC[N@H+](C2CC2)C(C2=CC=CC=C2)C1)C(=O)[O-]) `REAL300000086060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086060 none CCC(NN=C1CC[N@H+](C2CC2)C(C2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 1, 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, 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, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 3, 3, 1, 3, 3, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 3, 3, 1, 3, 3, 1, 1] 6 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 47, 40, 20, 46, 31] set([0, 1, 2, 11, 12, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 28 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: REAL300000086060 none CCC(NN=C1CC[N@H+](C2CC2)C(C2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 1, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 3, 3, 3, 3, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 3, 3] 6 rigid atoms, others: [45, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) total number of confs: 25 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086060 none CCC(NN=C1CC[N@H+](C2CC2)C(C2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 1, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4] 6 rigid atoms, others: [35, 36, 37, 38, 39, 8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 17 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086060 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086060/1 /scratch/stefan/7769667/working/building/REAL300000086060 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/61 `/scratch/stefan/7769667/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC[N@@H+](C2CC2)C(C2=CC=CC=C2)C1)C(=O)[O-]) `REAL300000086060.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086060/1/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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086060 none CCC(NN=C1CC[N@@H+](C2CC2)C(C2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 1, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 2, 2, 2, 2, 2, 1, 10, 11, 11, 13, 13, 13, 13, 13, 10, 6, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 1, 1] 13 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 47, 40, 20, 46, 31] set([0, 1, 2, 11, 12, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 64 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: REAL300000086060 none CCC(NN=C1CC[N@@H+](C2CC2)C(C2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 1, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 6, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 10, 11, 11, 13, 13, 13, 13, 13, 10, 6, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 1, 1, 1, 1, 1, 2, 2] 13 rigid atoms, others: [45, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) total number of confs: 62 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086060 none CCC(NN=C1CC[N@@H+](C2CC2)C(C2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 1, 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, 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, 12, 7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 12, 13, 13, 13, 13, 13, 13, 13, 12, 7, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3] 13 rigid atoms, others: [35, 36, 37, 38, 39, 8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 57 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086060 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086060 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086060/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086060/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086060 Building REAL300000086061 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086061' /scratch/stefan/7769667/working/building/REAL300000086061 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086061 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086061/0 /scratch/stefan/7769667/working/building/REAL300000086061 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/62 `/scratch/stefan/7769667/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C(=O)NC2=CC([O-])=C(Br)C=C21)C(=O)[O-]) `REAL300000086061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086061 none CCC(NN=C1C(=O)NC2=CC([O-])=C(Br)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 13, 13, 13, 13, 13, 10, 5, 1, 1, 1] 13 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29] set([0, 1, 2, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086061 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086061/1 /scratch/stefan/7769667/working/building/REAL300000086061 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/63 `/scratch/stefan/7769667/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C(=O)NC2=CC(O)=C(Br)C=C21)C(=O)[O-]) `REAL300000086061.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086061 none CCC(NN=C1C(=O)NC2=CC(O)=C(Br)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', '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, 5, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [19, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 15, 15, 19, 19, 19, 19, 19, 14, 6, 1, 1, 2, 1] 38 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 30] set([0, 1, 2, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086061 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086061 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086061/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086061/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086061 Building REAL300000086062 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086062' /scratch/stefan/7769667/working/building/REAL300000086062 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086062 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086062/0 /scratch/stefan/7769667/working/building/REAL300000086062 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/64 `/scratch/stefan/7769667/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC(C)(C)OC2=CC(OC)=CC=C21)C(=O)[O-]) `REAL300000086062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086062 none CCC(NN=C1CC(C)(C)OC2=CC(OC)=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 20, 25, 25, 33, 33, 33, 33, 33, 20, 7, 1, 1, 2, 2, 2, 2, 2, 2, 1, 2, 3, 3, 1, 1] 33 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 42, 41, 29, 30, 37] set([0, 1, 2, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 179 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086062 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086062 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086062/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086062 Building REAL300000086063 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086063' /scratch/stefan/7769667/working/building/REAL300000086063 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086063 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086063/0 /scratch/stefan/7769667/working/building/REAL300000086063 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/65 `/scratch/stefan/7769667/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(N2CCCCC2)C(Br)=C1)C(=O)[O-]) `REAL300000086063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086063 none CCC(NN=CC1=CC=C(N2CCCCC2)C(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 5, 1, 17, 1, 1, 11, 11, 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, 4, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [51, 43, 29, 9, 9, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 43, 46, 46, 51, 51, 51, 51, 51, 43, 28, 9, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1] 52 rigid atoms, others: [5, 6, 7, 8, 9, 10, 16, 17, 18, 42, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 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: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086063 none CCC(NN=CC1=CC=C(N2CCCCC2)C(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 5, 1, 17, 1, 1, 11, 11, 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, 4, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [51, 44, 33, 15, 10, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 44, 46, 46, 51, 51, 51, 52, 52, 44, 32, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3] 52 rigid atoms, others: [32, 33, 34, 35, 36, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 38, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42]) total number of confs: 204 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086063 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086063 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086063/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086063 Building REAL300000086064 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086064' /scratch/stefan/7769667/working/building/REAL300000086064 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086064 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086064/0 /scratch/stefan/7769667/working/building/REAL300000086064 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/66 `/scratch/stefan/7769667/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(O)=C1Br)C(=O)[O-]) `REAL300000086064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086064 none CCC(NN=CC1=CC=CC(O)=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [48, 36, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 48, 48, 48, 48, 48, 36, 23, 7, 1, 1, 1, 2] 96 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086064 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086064/1 /scratch/stefan/7769667/working/building/REAL300000086064 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/67 `/scratch/stefan/7769667/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC([O-])=C1Br)C(=O)[O-]) `REAL300000086064.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086064 none CCC(NN=CC1=CC=CC([O-])=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 21, 15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 24, 24, 30, 30, 30, 30, 30, 21, 15, 4, 1, 1, 1] 30 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086064 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086064 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086064/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086064/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086064 Building REAL300000086065 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086065' /scratch/stefan/7769667/working/building/REAL300000086065 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086065 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086065/0 /scratch/stefan/7769667/working/building/REAL300000086065 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/68 `/scratch/stefan/7769667/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CC(C)(C)C)C1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300000086065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086065 none CCC(NN=C(CC(C)(C)C)C1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 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: [34, 26, 14, 5, 5, 1, 5, 7, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 26, 28, 28, 34, 34, 34, 34, 34, 26, 14, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1] 48 rigid atoms, others: [5, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 186 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086065 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086065 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086065/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086065 Building REAL300000086066 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086066' /scratch/stefan/7769667/working/building/REAL300000086066 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086066 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086066/0 /scratch/stefan/7769667/working/building/REAL300000086066 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/69 `/scratch/stefan/7769667/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC=CC1=CC=C(OCC2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300000086066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086066 none CCC(NN=CC=CC1=CC=C(OCC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', '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', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [31, 18, 10, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 2, 10, 22, 22, 10, 22, 22, 1, 1, 18, 26, 26, 31, 31, 31, 31, 31, 18, 10, 4, 3, 3, 1, 1, 10, 10, 22, 22, 10, 22, 22, 1, 1] 94 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 45, 44, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 241 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086066 none CCC(NN=CC=CC1=CC=C(OCC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', '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', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 81, 56, 43, 43, 42, 42, 22, 22, 22, 22, 11, 3, 1, 1, 1, 1, 1, 1, 1, 22, 22, 81, 94, 94, 94, 94, 94, 94, 94, 81, 56, 43, 42, 42, 22, 22, 3, 3, 1, 1, 1, 1, 1, 22, 22] 94 rigid atoms, others: [39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45]) total number of confs: 430 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086066 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086066 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086066/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086066 Building REAL300000086067 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086067' /scratch/stefan/7769667/working/building/REAL300000086067 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086067 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086067/0 /scratch/stefan/7769667/working/building/REAL300000086067 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/70 `/scratch/stefan/7769667/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C2=CC=CC=C2C)=CC=C1OC)C(=O)[O-]) `REAL300000086067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086067 none CCC(NN=CC1=CC(C2=CC=CC=C2C)=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', '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.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 11, 11, 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, 4, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 32, 10, 10, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 1, 1, 1, 1, 3, 61, 82, 82, 91, 91, 91, 91, 91, 61, 32, 10, 1, 7, 7, 6, 7, 7, 7, 7, 1, 1, 3, 3, 3] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17, 18, 19, 41, 40] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 476 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086067 none CCC(NN=CC1=CC(C2=CC=CC=C2C)=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', '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.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 11, 11, 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, 4, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 161, 108, 30, 30, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 19, 161, 187, 187, 194, 194, 194, 194, 194, 161, 108, 30, 7, 1, 1, 1, 1, 2, 2, 2, 7, 7, 19, 19, 19] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 850 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086067 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086067 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086067/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086067 Building REAL300000086068 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086068' /scratch/stefan/7769667/working/building/REAL300000086068 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086068 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086068/0 /scratch/stefan/7769667/working/building/REAL300000086068 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/71 `/scratch/stefan/7769667/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC(C2=CC=CC=C2)=NN1C)C(=O)[O-]) `REAL300000086068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086068 none CCC(NN=C(C)C1=CC(C2=CC=CC=C2)=NN1C)C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 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, 25, 14, 4, 4, 1, 4, 1, 1, 1, 1, 6, 6, 2, 6, 6, 1, 1, 1, 25, 29, 29, 35, 35, 35, 35, 35, 25, 14, 4, 4, 4, 1, 6, 6, 2, 6, 6, 2, 2, 2] 39 rigid atoms, others: [32, 5, 7, 8, 9, 10, 16, 17, 18] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086068 none CCC(NN=C(C)C1=CC(C2=CC=CC=C2)=NN1C)C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 35, 27, 11, 11, 6, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 35, 39, 39, 39, 39, 39, 39, 39, 35, 27, 11, 11, 11, 6, 1, 1, 1, 1, 1, 6, 6, 6] 39 rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086068 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086068 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086068/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086068 Building REAL300000086069 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086069' /scratch/stefan/7769667/working/building/REAL300000086069 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086069 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086069/0 /scratch/stefan/7769667/working/building/REAL300000086069 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/72 `/scratch/stefan/7769667/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(C)N=C1C1=CC=C(F)C=C1)C(=O)[O-]) `REAL300000086069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086069 none CCC(NN=CC1=CN(C)N=C1C1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 5, 8, 8, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [62, 48, 28, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 2, 2, 6, 6, 48, 56, 56, 62, 62, 62, 62, 62, 48, 28, 11, 1, 2, 2, 2, 6, 6, 6, 6] 81 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 305 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086069 none CCC(NN=CC1=CN(C)N=C1C1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 5, 8, 8, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 74, 55, 27, 27, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 74, 81, 81, 81, 81, 81, 81, 81, 74, 55, 27, 6, 6, 6, 6, 1, 1, 1, 1] 81 rigid atoms, others: [34, 35, 36, 37, 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, 33]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086069 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086069 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086069/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086069 Building REAL300000086070 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086070' /scratch/stefan/7769667/working/building/REAL300000086070 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086070 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086070/0 /scratch/stefan/7769667/working/building/REAL300000086070 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/73 `/scratch/stefan/7769667/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC(C2=CC=C(Br)C=C2F)C1)C(=O)[O-]) `REAL300000086070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086070 none CCC(NN=C1CC(C2=CC=C(Br)C=C2F)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', '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, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 17, 1, 1, 15, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 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: [39, 25, 9, 1, 1, 1, 1, 1, 1, 8, 8, 4, 7, 8, 8, 8, 1, 25, 33, 33, 39, 39, 39, 39, 39, 25, 9, 1, 1, 1, 8, 8, 8, 1, 1] 85 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 16, 27, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32]) total number of confs: 228 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086070 none CCC(NN=C1CC(C2=CC=C(Br)C=C2F)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', '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, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 17, 1, 1, 15, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [85, 68, 41, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 68, 72, 72, 85, 85, 85, 85, 85, 68, 41, 8, 8, 8, 1, 1, 1, 8, 8] 85 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 365 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086070 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086070 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086070/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086070 Building REAL300000086071 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086071' /scratch/stefan/7769667/working/building/REAL300000086071 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086071 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086071/0 /scratch/stefan/7769667/working/building/REAL300000086071 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/74 `/scratch/stefan/7769667/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CN1CC(=O)OC(C)(C)C)C(=O)[O-]) `REAL300000086071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086071 none CCC(NN=CC1=CC=CN1CC(=O)OC(C)(C)C)C(=O)[O-] 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', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 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, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [22, 13, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 22, 22, 29, 29, 29, 29, 13, 16, 16, 22, 22, 22, 22, 22, 13, 8, 4, 1, 1, 1, 3, 3, 29, 29, 29, 29, 29, 29, 29, 29, 29] 59 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 4, 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, 43]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086071 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086071 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086071/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086071 Building REAL300000086072 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086072' /scratch/stefan/7769667/working/building/REAL300000086072 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086072 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086072/0 /scratch/stefan/7769667/working/building/REAL300000086072 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/75 `/scratch/stefan/7769667/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(C2=CC=CC(F)=C2)N=C1C)C(=O)[O-]) `REAL300000086072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086072 none CCC(NN=CC1=CN(C2=CC=CC(F)=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'C.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 9, 6, 6, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 3, 1, 1, 1, 11, 11, 11, 12, 12, 12, 12, 12, 11, 9, 6, 1, 3, 3, 2, 3, 2, 2, 2] 20 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086072 none CCC(NN=CC1=CN(C2=CC=CC(F)=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'C.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 19, 16, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 19, 19, 19, 20, 20, 20, 20, 20, 19, 16, 11, 3, 1, 1, 1, 1, 3, 3, 3] 20 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086072 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086072 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086072/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086072 Building REAL300000086073 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086073' /scratch/stefan/7769667/working/building/REAL300000086073 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086073 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086073/0 /scratch/stefan/7769667/working/building/REAL300000086073 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/76 `/scratch/stefan/7769667/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CSC(C2=CC=CC=C2)=N1)C(=O)[O-]) `REAL300000086073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086073 none CCC(NN=C(C)C1=CSC(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 5, 5, 8, 8, 1, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 6, 3, 3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 9, 9, 9, 14, 14, 14, 14, 14, 9, 6, 4, 4, 4, 1, 4, 4, 1, 4, 4] 14 rigid atoms, others: [5, 7, 8, 9, 10, 11, 17, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086073 none CCC(NN=C(C)C1=CSC(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 5, 5, 8, 8, 1, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 10, 6, 6, 4, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 10, 14, 14, 14, 14, 14, 10, 10, 6, 6, 6, 3, 1, 1, 1, 1, 1] 14 rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 52 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086073 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086073 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086073/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086073 Building REAL300000086074 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086074' /scratch/stefan/7769667/working/building/REAL300000086074 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086074 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086074/0 /scratch/stefan/7769667/working/building/REAL300000086074 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/77 `/scratch/stefan/7769667/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(F)=CC(Br)=C1)C(=O)[O-]) `REAL300000086074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086074 none CCC(NN=CC1=CC(F)=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [81, 53, 32, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 58, 58, 81, 81, 81, 81, 81, 53, 32, 7, 1, 1, 1] 83 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086074 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086074 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086074/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086074 Building REAL300000086075 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086075' /scratch/stefan/7769667/working/building/REAL300000086075 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086075 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086075/0 /scratch/stefan/7769667/working/building/REAL300000086075 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/78 `/scratch/stefan/7769667/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=NC(Br)=CS1)C(=O)[O-]) `REAL300000086075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086075 none CCC(NN=C(C)C1=NC(Br)=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'C.2', 'Br', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 8, 1, 17, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 38, 40, 40, 50, 50, 50, 50, 50, 38, 25, 10, 10, 10, 1] 50 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086075 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086075 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086075/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086075 Building REAL300000086076 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086076' /scratch/stefan/7769667/working/building/REAL300000086076 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086076 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086076/0 /scratch/stefan/7769667/working/building/REAL300000086076 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/79 `/scratch/stefan/7769667/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCCC(C2=CC=C(Cl)C=C2)C1)C(=O)[O-]) `REAL300000086076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086076 none CCC(NN=C1CCCC(C2=CC=C(Cl)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [33, 23, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 23, 29, 29, 33, 33, 33, 33, 33, 23, 8, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1] 34 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 39, 17, 40, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 167 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086076 none CCC(NN=C1CCCC(C2=CC=C(Cl)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 28, 16, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 28, 32, 32, 34, 34, 34, 34, 34, 28, 16, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4] 34 rigid atoms, others: [35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40]) total number of confs: 148 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086076 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086076 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086076/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086076 Building REAL300000086077 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086077' /scratch/stefan/7769667/working/building/REAL300000086077 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086077 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086077/0 /scratch/stefan/7769667/working/building/REAL300000086077 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/80 `/scratch/stefan/7769667/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(CNN=C(CC)C(=O)[O-])=CC=C1OC(=O)CC) `REAL300000086077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086077 none CCOC1=CC(CNN=C(CC)C(=O)[O-])=CC=C1OC(=O)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 5, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 12, 1, 11, 5, 5, 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, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 1, 1, 1, 1, 1, 2, 7, 7, 7, 31, 7, 9, 9, 1, 1, 1, 1, 7, 21, 21, 48, 15, 15, 15, 15, 15, 1, 2, 2, 7, 31, 31, 31, 31, 31, 1, 1, 48, 48, 48, 48, 48] 107 rigid atoms, others: [2, 3, 4, 5, 6, 15, 16, 17, 18, 38, 28, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086077 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086077 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086077/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086077 Building REAL300000086078 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086078' /scratch/stefan/7769667/working/building/REAL300000086078 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086078 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086078/0 /scratch/stefan/7769667/working/building/REAL300000086078 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/81 `/scratch/stefan/7769667/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(F)C=C1I)C(=O)[O-]) `REAL300000086078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086078 none CCC(NN=CC1=CC=C(F)C=C1I)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'I', 'C.2', 'O.co2', 'O.co2', '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, 15, 1, 1, 18, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [53, 38, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 42, 42, 53, 53, 53, 53, 53, 38, 29, 10, 1, 1, 1] 55 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086078 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086078 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086078/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086078 Building REAL300000086079 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086079' /scratch/stefan/7769667/working/building/REAL300000086079 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086079 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086079/0 /scratch/stefan/7769667/working/building/REAL300000086079 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/82 `/scratch/stefan/7769667/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C)N(CC2=CC=CC=C2)C(C)=C1)C(=O)[O-]) `REAL300000086079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086079 none CCC(NN=CC1=C(C)N(CC2=CC=CC=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 46, 24, 6, 6, 1, 1, 1, 1, 1, 1, 7, 13, 13, 7, 13, 13, 1, 1, 1, 46, 60, 60, 73, 73, 73, 73, 73, 46, 24, 6, 2, 2, 2, 7, 7, 13, 13, 13, 13, 13, 2, 2, 2, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 44, 17, 18, 19] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 20, 21, 22, 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: 437 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086079 none CCC(NN=CC1=C(C)N(CC2=CC=CC=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 167, 120, 53, 53, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 167, 201, 201, 201, 201, 201, 201, 201, 167, 120, 53, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 13, 13, 13, 13] 201 rigid atoms, others: [36, 37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44]) total number of confs: 923 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086079 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086079 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086079/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086079 Building REAL300000086080 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086080' /scratch/stefan/7769667/working/building/REAL300000086080 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086080 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086080/0 /scratch/stefan/7769667/working/building/REAL300000086080 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/83 `/scratch/stefan/7769667/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC(NC(=O)OC(C)(C)C)C1(C)C)C(=O)[O-]) `REAL300000086080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086080 none CCC(NN=C1CC(NC(=O)OC(C)(C)C)C1(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 7, 1, 1, 1, 1, 1, 1, 7, 13, 13, 34, 40, 40, 40, 1, 1, 1, 21, 36, 36, 41, 41, 41, 41, 41, 21, 7, 1, 1, 1, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 357 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086080 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086080 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086080/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086080 Building REAL300000086081 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086081' /scratch/stefan/7769667/working/building/REAL300000086081 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086081 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086081/0 /scratch/stefan/7769667/working/building/REAL300000086081 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/84 `/scratch/stefan/7769667/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C2=CC=CC=C2)N(C2CCCC2)N=C1)C(=O)[O-]) `REAL300000086081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086081 none CCC(NN=CC1=C(C2=CC=CC=C2)N(C2CCCC2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 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, 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: [60, 40, 18, 6, 6, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 6, 6, 6, 6, 1, 1, 40, 52, 52, 60, 60, 60, 60, 60, 40, 18, 6, 4, 4, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1] 96 rigid atoms, others: [5, 6, 7, 8, 14, 15, 20, 21, 47] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 16, 17, 18, 19, 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]) total number of confs: 332 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086081 none CCC(NN=CC1=C(C2=CC=CC=C2)N(C2CCCC2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 87, 61, 26, 26, 6, 6, 6, 6, 14, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 6, 6, 87, 95, 95, 96, 96, 96, 96, 96, 87, 61, 26, 14, 14, 10, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6] 96 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 417 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086081 none CCC(NN=CC1=C(C2=CC=CC=C2)N(C2CCCC2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 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, 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: [77, 60, 37, 15, 15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 4, 4, 60, 70, 70, 77, 77, 77, 77, 77, 60, 37, 15, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 96 rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 378 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086081 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086081 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086081/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086081 Building REAL300000086082 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086082' /scratch/stefan/7769667/working/building/REAL300000086082 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086082 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086082/0 /scratch/stefan/7769667/working/building/REAL300000086082 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/85 `/scratch/stefan/7769667/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCCCC2=CC=C([N+](=O)[O-])C=C21)C(=O)[O-]) `REAL300000086082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086082 none CCC(NN=C1CCCCC2=CC=C([N+](=O)[O-])C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 18, 18, 18, 18, 18, 18, 18, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 18 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086082 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086082 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086082/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086082 Building REAL300000086083 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086083' /scratch/stefan/7769667/working/building/REAL300000086083 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086083 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086083/0 /scratch/stefan/7769667/working/building/REAL300000086083 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/86 `/scratch/stefan/7769667/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCN(C(=O)OC(C)(C)C)C(C)C1)C(=O)[O-]) `REAL300000086083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086083 none CCC(NN=C1CCN(C(=O)OC(C)(C)C)C(C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 3, 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, 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: [42, 25, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 18, 21, 21, 21, 1, 1, 1, 25, 37, 37, 42, 42, 42, 42, 42, 25, 7, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 1, 1] 109 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 42, 46, 47, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 276 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086083 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086083 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086083/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086083 Building REAL300000086084 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086084' /scratch/stefan/7769667/working/building/REAL300000086084 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086084 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086084/0 /scratch/stefan/7769667/working/building/REAL300000086084 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/87 `/scratch/stefan/7769667/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC2CN(C(=O)OC(C)(C)C)CC2C1)C(=O)[O-]) `REAL300000086084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086084 none CCC(NN=C1CCC2CN(C(=O)OC(C)(C)C)CC2C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [39, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 23, 24, 23, 1, 1, 1, 24, 35, 35, 39, 39, 39, 39, 39, 24, 7, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1] 86 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 268 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086084 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086084 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086084/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086084 Building REAL300000086085 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086085' /scratch/stefan/7769667/working/building/REAL300000086085 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086085 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086085/0 /scratch/stefan/7769667/working/building/REAL300000086085 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/88 `/scratch/stefan/7769667/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCN(C(=O)OCC2=CC=CC=C2)C1)C(=O)[O-]) `REAL300000086085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086085 none CCC(NN=C1CCN(C(=O)OCC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 17, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 27, 61, 61, 27, 61, 61, 1, 17, 29, 29, 33, 33, 33, 33, 33, 17, 6, 1, 1, 1, 1, 27, 27, 61, 61, 27, 61, 61, 1, 1] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 42, 19, 41, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 415 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086085 none CCC(NN=C1CCN(C(=O)OCC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 150, 61, 61, 61, 61, 61, 40, 19, 40, 3, 1, 1, 1, 1, 1, 1, 1, 61, 195, 201, 201, 201, 201, 201, 201, 201, 195, 150, 61, 61, 61, 61, 3, 3, 1, 1, 1, 1, 1, 61, 61] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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, 35, 41, 42]) total number of confs: 728 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086085 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086085 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086085/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086085 Building REAL300000086086 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086086' /scratch/stefan/7769667/working/building/REAL300000086086 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086086 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086086/0 /scratch/stefan/7769667/working/building/REAL300000086086 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/89 `/scratch/stefan/7769667/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(Br)C=N1)C(=O)[O-]) `REAL300000086086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086086 none CCC(NN=C(C)C1=CC=C(Br)C=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 31, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 31, 32, 32, 37, 37, 37, 37, 37, 31, 19, 8, 8, 8, 1, 1, 1] 37 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086086 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086086 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086086/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086086 Building REAL300000086087 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086087' /scratch/stefan/7769667/working/building/REAL300000086087 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086087 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086087/0 /scratch/stefan/7769667/working/building/REAL300000086087 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/90 `/scratch/stefan/7769667/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=CN=C1Cl)C(=O)[O-]) `REAL300000086087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086087 none CCC(NN=CC1=CC(Br)=CN=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 8, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 36, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 47, 47, 47, 47, 47, 36, 26, 8, 1, 1] 47 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086087 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086087 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086087/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086087 Building REAL300000086088 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086088' /scratch/stefan/7769667/working/building/REAL300000086088 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086088 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086088/0 /scratch/stefan/7769667/working/building/REAL300000086088 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/91 `/scratch/stefan/7769667/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(OC(F)F)=CC=C1Br)C(=O)[O-]) `REAL300000086088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086088 none CCC(NN=CC1=CC(OC(F)F)=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', '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, 12, 5, 15, 15, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [23, 14, 7, 4, 4, 1, 1, 1, 1, 1, 8, 22, 22, 1, 1, 1, 1, 14, 18, 18, 23, 23, 23, 23, 23, 14, 7, 4, 1, 22, 1, 1] 51 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15, 16, 28, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086088 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086088 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086088/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086088 Building REAL300000086089 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086089' /scratch/stefan/7769667/working/building/REAL300000086089 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086089 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086089/0 /scratch/stefan/7769667/working/building/REAL300000086089 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/92 `/scratch/stefan/7769667/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300000086089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086089 none CCC(NN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 12, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 36, 53, 53, 36, 49, 49, 36, 49, 49, 1, 12, 14, 14, 20, 20, 20, 20, 20, 12, 9, 4, 1, 1, 1, 36, 49, 49, 36, 49, 49, 1] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 43, 22] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 347 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086089 none CCC(NN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 159, 144, 91, 91, 49, 49, 49, 49, 49, 9, 3, 1, 3, 4, 4, 1, 1, 1, 1, 1, 1, 49, 159, 169, 169, 199, 199, 199, 199, 199, 159, 144, 91, 49, 49, 49, 3, 1, 1, 1, 1, 1, 49] 201 rigid atoms, others: [38, 39, 40, 41, 42, 12, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43]) total number of confs: 769 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086089 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086089 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086089/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086089 Building REAL300000086090 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086090' /scratch/stefan/7769667/working/building/REAL300000086090 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086090 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086090/0 /scratch/stefan/7769667/working/building/REAL300000086090 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/93 `/scratch/stefan/7769667/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN=C(C2=CC=C(C)C(C)=C2)S1)C(=O)[O-]) `REAL300000086090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086090 none CCC(NN=CC1=CN=C(C2=CC=C(C)C(C)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.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, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 5, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 8, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 5, 4, 1, 9, 9, 9, 13, 13, 13, 13, 13, 9, 8, 5, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5] 18 rigid atoms, others: [5, 6, 7, 8, 9, 10, 18, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086090 none CCC(NN=CC1=CN=C(C2=CC=C(C)C(C)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.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, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 5, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 16, 11, 11, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 11, 4, 1, 1, 2, 2, 2, 2, 2, 2, 1] 18 rigid atoms, others: [32, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 65 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086090 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086090 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086090/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086090 Building REAL300000086091 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086091' /scratch/stefan/7769667/working/building/REAL300000086091 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086091 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086091/0 /scratch/stefan/7769667/working/building/REAL300000086091 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/94 `/scratch/stefan/7769667/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCCC(NC(=O)OC(C)(C)C)C1)C(=O)[O-]) `REAL300000086091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086091 none CCC(NN=C1CCCC(NC(=O)OC(C)(C)C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 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, 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: [38, 22, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 37, 48, 48, 48, 1, 22, 34, 34, 38, 38, 38, 38, 38, 22, 8, 1, 1, 1, 1, 1, 1, 1, 7, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1] 198 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 46, 47, 18, 35, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 345 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086091 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086091 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086091/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086091 Building REAL300000086092 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086092' /scratch/stefan/7769667/working/building/REAL300000086092 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086092 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086092/0 /scratch/stefan/7769667/working/building/REAL300000086092 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/95 `/scratch/stefan/7769667/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(C2=CC=CC=C2F)N=C1C)C(=O)[O-]) `REAL300000086092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086092 none CCC(NN=CC1=CN(C2=CC=CC=C2F)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [78, 54, 23, 7, 7, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 1, 1, 1, 54, 67, 67, 78, 78, 78, 78, 78, 54, 23, 7, 1, 7, 7, 6, 7, 2, 2, 2] 101 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086092 none CCC(NN=CC1=CN(C2=CC=CC=C2F)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 86, 68, 33, 33, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 86, 101, 101, 101, 101, 101, 101, 101, 86, 68, 33, 7, 1, 1, 1, 1, 7, 7, 7] 101 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 432 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086092 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086092 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086092/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086092 Building REAL300000086093 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086093' /scratch/stefan/7769667/working/building/REAL300000086093 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086093 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086093/0 /scratch/stefan/7769667/working/building/REAL300000086093 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/96 `/scratch/stefan/7769667/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(C2=CC=CC=C2Br)N=C1C)C(=O)[O-]) `REAL300000086093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086093 none CCC(NN=CC1=CN(C2=CC=CC=C2Br)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'C.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 8, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 10, 10, 10, 14, 14, 14, 14, 14, 10, 8, 5, 1, 7, 7, 7, 7, 2, 2, 2] 27 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086093 none CCC(NN=CC1=CN(C2=CC=CC=C2Br)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'C.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 23, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 25, 25, 27, 27, 27, 27, 27, 25, 23, 16, 7, 1, 1, 1, 1, 7, 7, 7] 27 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086093 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086093 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086093/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086093 Building REAL300000086094 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086094' /scratch/stefan/7769667/working/building/REAL300000086094 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086094 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086094/0 /scratch/stefan/7769667/working/building/REAL300000086094 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/97 `/scratch/stefan/7769667/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(C2=CC=CC=C2Cl)N=C1C)C(=O)[O-]) `REAL300000086094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086094 none CCC(NN=CC1=CN(C2=CC=CC=C2Cl)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 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: [11, 10, 7, 4, 4, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 10, 10, 10, 11, 11, 11, 11, 11, 10, 7, 4, 1, 5, 5, 5, 5, 2, 2, 2] 21 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086094 none CCC(NN=CC1=CN(C2=CC=CC=C2Cl)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 19, 15, 10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 21, 21, 21, 21, 21, 19, 15, 10, 5, 1, 1, 1, 1, 5, 5, 5] 21 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086094 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086094 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086094/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086094 Building REAL300000086095 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086095' /scratch/stefan/7769667/working/building/REAL300000086095 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086095 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086095/0 /scratch/stefan/7769667/working/building/REAL300000086095 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/98 `/scratch/stefan/7769667/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(C2=CC=C(C)C=C2)N=C1C)C(=O)[O-]) `REAL300000086095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086095 none CCC(NN=CC1=CN(C2=CC=C(C)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 10, 6, 6, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 2, 1, 1, 1, 13, 13, 13, 14, 14, 14, 14, 14, 13, 10, 6, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 14 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086095 none CCC(NN=CC1=CN(C2=CC=C(C)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 10, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 13, 13, 14, 14, 14, 14, 14, 13, 10, 7, 2, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2] 14 rigid atoms, others: [32, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39, 40]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086095 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086095 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086095/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086095 Building REAL300000086096 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086096' /scratch/stefan/7769667/working/building/REAL300000086096 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086096 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086096/0 /scratch/stefan/7769667/working/building/REAL300000086096 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/99 `/scratch/stefan/7769667/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(C2=CC=CC(Br)=C2)N=C1C)C(=O)[O-]) `REAL300000086096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086096 none CCC(NN=CC1=CN(C2=CC=CC(Br)=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 9, 6, 6, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 3, 1, 1, 1, 11, 11, 11, 12, 12, 12, 12, 12, 11, 9, 6, 1, 3, 3, 2, 3, 2, 2, 2] 20 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086096 none CCC(NN=CC1=CN(C2=CC=CC(Br)=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 19, 16, 11, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 19, 19, 19, 20, 20, 20, 20, 20, 19, 16, 11, 3, 1, 1, 1, 1, 3, 3, 3] 20 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086096 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086096 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086096/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086096 Building REAL300000086097 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086097' /scratch/stefan/7769667/working/building/REAL300000086097 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086097 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086097/0 /scratch/stefan/7769667/working/building/REAL300000086097 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/100 `/scratch/stefan/7769667/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C2CC2)N(C2=CC=CC=C2)N=N1)C(=O)[O-]) `REAL300000086097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086097 none CCC(NN=CC1=C(C2CC2)N(C2=CC=CC=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 5, 5, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [24, 22, 12, 6, 6, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 3, 3, 1, 1, 22, 24, 24, 24, 24, 24, 24, 24, 22, 12, 6, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3] 26 rigid atoms, others: [5, 6, 7, 8, 11, 12, 18, 19] set([0, 1, 2, 3, 4, 9, 10, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086097 none CCC(NN=CC1=C(C2CC2)N(C2=CC=CC=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 5, 5, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 14, 7, 7, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 24, 26, 26, 26, 26, 26, 26, 26, 24, 14, 7, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 26 rigid atoms, others: [36, 37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 102 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086097 none CCC(NN=CC1=C(C2CC2)N(C2=CC=CC=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 5, 5, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 14, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 26, 26, 26, 26, 26, 26, 26, 24, 14, 7, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 26 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086097 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086097 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086097/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086097 Building REAL300000086098 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086098' /scratch/stefan/7769667/working/building/REAL300000086098 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086098 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086098/0 /scratch/stefan/7769667/working/building/REAL300000086098 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/101 `/scratch/stefan/7769667/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C(=O)NC2=CC(Cl)=C(Br)C=C21)C(=O)[O-]) `REAL300000086098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086098 none CCC(NN=C1C(=O)NC2=CC(Cl)=C(Br)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 16, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 16, 16, 20, 20, 20, 20, 20, 15, 6, 1, 1, 1] 20 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29] set([0, 1, 2, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086098 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086098 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086098/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086098 Building REAL300000086099 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086099' /scratch/stefan/7769667/working/building/REAL300000086099 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086099 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086099/0 /scratch/stefan/7769667/working/building/REAL300000086099 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/102 `/scratch/stefan/7769667/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C(=O)NC2=C1C=CC(Br)=C2C)C(=O)[O-]) `REAL300000086099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086099 none CCC(NN=C1C(=O)NC2=C1C=CC(Br)=C2C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 1, 17, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 15, 15, 18, 18, 18, 18, 18, 14, 6, 1, 1, 1, 2, 2, 2] 18 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29] set([0, 1, 2, 32, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086099 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086099 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086099/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086099 Building REAL300000086100 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086100' /scratch/stefan/7769667/working/building/REAL300000086100 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086100 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086100/0 /scratch/stefan/7769667/working/building/REAL300000086100 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/103 `/scratch/stefan/7769667/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCN(C(=O)OC(C)(C)C)C(C)(C)C1)C(=O)[O-]) `REAL300000086100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086100 none CCC(NN=C1CCN(C(=O)OC(C)(C)C)C(C)(C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 3, 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, 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: [40, 26, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 18, 18, 18, 1, 1, 1, 1, 26, 37, 37, 40, 40, 40, 40, 40, 26, 7, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 1, 1] 94 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 50, 16, 17, 18, 19, 49, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 259 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086100 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086100 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086100/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086100 Building REAL300000086101 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086101' /scratch/stefan/7769667/working/building/REAL300000086101 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086101 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086101/0 /scratch/stefan/7769667/working/building/REAL300000086101 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/104 `/scratch/stefan/7769667/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC(Br)=CC(OC)=C1O)C(=O)[O-]) `REAL300000086101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086101 none CCC(NN=C(C)C1=CC(Br)=CC(OC)=C1O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 17, 1, 1, 12, 5, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 202 conformations in input total number of sets (complete confs): 202 using faster count positions algorithm for large data unique positions, atoms: [79, 52, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 52, 60, 60, 79, 79, 79, 79, 79, 52, 31, 10, 10, 10, 1, 1, 4, 4, 4, 2] 202 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 372 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086101 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086101 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086101/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086101 Building REAL300000086102 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086102' /scratch/stefan/7769667/working/building/REAL300000086102 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300000086102 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086102/0 /scratch/stefan/7769667/working/building/REAL300000086102 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/105 `/scratch/stefan/7769667/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CN(CC2=CC=CC=C2)C(C)(C)C1)C(=O)[O-]) `REAL300000086102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086102 none CCC(NN=C1CN(CC2=CC=CC=C2)C(C)(C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 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, 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, 26, 7, 1, 1, 1, 1, 1, 1, 3, 5, 5, 3, 5, 5, 1, 1, 1, 1, 26, 36, 36, 40, 40, 40, 40, 40, 26, 7, 1, 1, 3, 3, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 1, 1] 56 rigid atoms, others: [3, 4, 5, 6, 7, 8, 44, 45, 15, 16, 17, 18, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 246 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086102 none CCC(NN=C1CN(CC2=CC=CC=C2)C(C)(C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 47, 23, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 47, 56, 56, 56, 56, 56, 56, 56, 47, 23, 5, 5, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5] 56 rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 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: 266 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086102 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086102/1 /scratch/stefan/7769667/working/building/REAL300000086102 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/106 `/scratch/stefan/7769667/working/3D/106' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C[N@H+](CC2=CC=CC=C2)C(C)(C)C1)C(=O)[O-]) `REAL300000086102.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086102 none CCC(NN=C1C[N@H+](CC2=CC=CC=C2)C(C)(C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 1, 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, 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, 14, 6, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 4, 6, 6, 1, 1, 1, 1, 14, 19, 19, 22, 22, 22, 22, 22, 14, 6, 1, 1, 4, 4, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 1, 1] 30 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 45, 46, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 149 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086102 none CCC(NN=C1C[N@H+](CC2=CC=CC=C2)C(C)(C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 1, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 14, 6, 6, 6, 6, 3, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 26, 30, 30, 30, 30, 30, 30, 30, 26, 14, 6, 6, 3, 3, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6] 30 rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 141 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086102 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `2' /scratch/stefan/7769667/working/building/REAL300000086102/2 /scratch/stefan/7769667/working/building/REAL300000086102 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 2 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/107 `/scratch/stefan/7769667/working/3D/107' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C[N@@H+](CC2=CC=CC=C2)C(C)(C)C1)C(=O)[O-]) `REAL300000086102.mol2' -> `2.mol2' `temp.mol2' -> `REAL300000086102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086102/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086102 none CCC(NN=C1C[N@@H+](CC2=CC=CC=C2)C(C)(C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 1, 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, 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: [10, 8, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 3, 5, 5, 1, 1, 1, 1, 8, 8, 8, 10, 10, 10, 10, 10, 8, 5, 1, 1, 3, 3, 5, 5, 3, 5, 5, 2, 2, 2, 2, 2, 2, 1, 1] 13 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 45, 46, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086102 none CCC(NN=C1C[N@@H+](CC2=CC=CC=C2)C(C)(C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 1, 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, 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, 12, 9, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 12, 13, 13, 13, 13, 13, 12, 9, 5, 5, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5] 13 rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 50 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086102 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086102 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 2: /scratch/stefan/7769667/working/building/REAL300000086102/2.* 0: /scratch/stefan/7769667/working/building/REAL300000086102/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086102/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086102 Building REAL300000086103 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086103' /scratch/stefan/7769667/working/building/REAL300000086103 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086103 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086103/0 /scratch/stefan/7769667/working/building/REAL300000086103 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/108 `/scratch/stefan/7769667/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC(C)(C)OC2=C(OC)C=CC=C12)C(=O)[O-]) `REAL300000086103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086103 none CCC(NN=C1CC(C)(C)OC2=C(OC)C=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 12, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [30, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 19, 24, 24, 30, 30, 30, 30, 30, 19, 8, 1, 1, 2, 2, 2, 2, 2, 2, 4, 4, 4, 1, 1, 1] 33 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 40, 18, 42, 17, 41, 29, 30] set([0, 1, 2, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086103 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086103 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086103/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086103 Building REAL300000086104 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086104' /scratch/stefan/7769667/working/building/REAL300000086104 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086104 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086104/0 /scratch/stefan/7769667/working/building/REAL300000086104 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/109 `/scratch/stefan/7769667/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCN(C(=O)OC(C)(C)C)C2(CC2)C1)C(=O)[O-]) `REAL300000086104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086104 none CCC(NN=C1CCN(C(=O)OC(C)(C)C)C2(CC2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [32, 20, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 14, 14, 14, 1, 1, 1, 1, 20, 28, 28, 32, 32, 32, 32, 32, 20, 8, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1] 79 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 43, 44, 45, 46, 47, 16, 17, 18, 19, 48, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086104 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086104 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086104/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086104 Building REAL300000086105 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086105' /scratch/stefan/7769667/working/building/REAL300000086105 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086105 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086105/0 /scratch/stefan/7769667/working/building/REAL300000086105 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/110 `/scratch/stefan/7769667/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(S(N)(=O)=O)C=C1F)C(=O)[O-]) `REAL300000086105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086105 none CCC(NN=CC1=CC=C(S(N)(=O)=O)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 14, 8, 11, 11, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 2, 2, 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: [57, 46, 28, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 46, 47, 47, 57, 57, 57, 57, 57, 46, 28, 7, 1, 1, 5, 5, 1] 131 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086105 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086105 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086105/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086105 Building REAL300000086106 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086106' /scratch/stefan/7769667/working/building/REAL300000086106 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086106 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086106/0 /scratch/stefan/7769667/working/building/REAL300000086106 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/111 `/scratch/stefan/7769667/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(O)C(Br)=C1)C(=O)[O-]) `REAL300000086106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086106 none CCC(NN=C(C)C1=CC=C(O)C(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 12, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [90, 64, 41, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 64, 69, 69, 90, 90, 90, 90, 90, 64, 41, 11, 11, 11, 1, 1, 2, 1] 180 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 372 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086106 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086106/1 /scratch/stefan/7769667/working/building/REAL300000086106 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/112 `/scratch/stefan/7769667/working/3D/112' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C([O-])C(Br)=C1)C(=O)[O-]) `REAL300000086106.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086106 none CCC(NN=C(C)C1=CC=C([O-])C(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 53, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 68, 68, 68, 68, 68, 53, 32, 11, 11, 11, 1, 1, 1] 68 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 257 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086106 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086106 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086106/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086106/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086106 Building REAL300000086107 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086107' /scratch/stefan/7769667/working/building/REAL300000086107 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086107 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086107/0 /scratch/stefan/7769667/working/building/REAL300000086107 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/113 `/scratch/stefan/7769667/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(OCC2=CC=C(F)C=C2F)=C1)C(=O)[O-]) `REAL300000086107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086107 none CCC(NN=CC1=CC=CC(OCC2=CC=C(F)C=C2F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 12, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 44, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 16, 3, 15, 16, 16, 16, 1, 44, 53, 53, 57, 57, 57, 57, 57, 44, 22, 6, 1, 1, 1, 3, 3, 16, 16, 16, 1] 201 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 41] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086107 none CCC(NN=CC1=CC=CC(OCC2=CC=C(F)C=C2F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 12, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 128, 63, 63, 16, 16, 15, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 63, 15, 16, 16, 8, 8, 1, 1, 1, 16] 201 rigid atoms, others: [38, 39, 40, 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, 41]) total number of confs: 767 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086107 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086107 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086107/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086107 Building REAL300000086108 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086108' /scratch/stefan/7769667/working/building/REAL300000086108 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086108 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086108/0 /scratch/stefan/7769667/working/building/REAL300000086108 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/114 `/scratch/stefan/7769667/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(C2=CC=CC(C)=C2)N=C1C)C(=O)[O-]) `REAL300000086108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086108 none CCC(NN=CC1=CN(C2=CC=CC(C)=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 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, 12, 9, 6, 6, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 3, 1, 1, 1, 12, 12, 12, 13, 13, 13, 13, 13, 12, 9, 6, 1, 3, 3, 2, 3, 3, 3, 3, 2, 2, 2] 25 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086108 none CCC(NN=CC1=CN(C2=CC=CC(C)=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 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, 23, 17, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 23, 23, 23, 25, 25, 25, 25, 25, 23, 17, 11, 3, 1, 1, 1, 2, 2, 2, 1, 3, 3, 3] 25 rigid atoms, others: [32, 33, 37, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 38, 39, 40]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086108 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086108 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086108/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086108 Building REAL300000086109 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086109' /scratch/stefan/7769667/working/building/REAL300000086109 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086109 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086109/0 /scratch/stefan/7769667/working/building/REAL300000086109 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/115 `/scratch/stefan/7769667/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(Br)C2=CC=CC=C2N1C)C(=O)[O-]) `REAL300000086109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086109 none CCC(NN=CC1=C(Br)C2=CC=CC=C2N1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 5, 8, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 39, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 41, 41, 47, 47, 47, 47, 47, 39, 23, 8, 1, 1, 1, 1, 2, 2, 2] 47 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 33, 32, 34, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086109 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086109 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086109/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086109 Building REAL300000086110 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086110' /scratch/stefan/7769667/working/building/REAL300000086110 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086110 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086110/0 /scratch/stefan/7769667/working/building/REAL300000086110 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/116 `/scratch/stefan/7769667/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[O-]) `REAL300000086110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086110 none CCC(NN=C(C)C1CN(C(=O)OC(C)(C)C)CCO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 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, 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, 31, 17, 7, 7, 1, 7, 1, 1, 1, 1, 2, 2, 10, 15, 15, 15, 1, 1, 1, 31, 41, 41, 46, 46, 46, 46, 46, 31, 17, 7, 7, 7, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1] 135 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 45, 46, 47, 48, 17, 18, 19] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 280 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086110 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086110 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086110/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086110 Building REAL300000086111 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086111' /scratch/stefan/7769667/working/building/REAL300000086111 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086111 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086111/0 /scratch/stefan/7769667/working/building/REAL300000086111 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/117 `/scratch/stefan/7769667/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1(S(=O)(=O)NC(C)(C)C)CC1)C(=O)[O-]) `REAL300000086111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086111 none CCC(NN=CC1(S(=O)(=O)NC(C)(C)C)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 6, 4, 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, 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: [103, 80, 54, 13, 13, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 1, 1, 80, 95, 95, 103, 103, 103, 103, 103, 80, 54, 13, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 119 rigid atoms, others: [5, 38, 7, 40, 41, 39, 15, 16, 6] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 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: 472 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086111 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086111 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086111/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086111 Building REAL300000086112 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086112' /scratch/stefan/7769667/working/building/REAL300000086112 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086112 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086112/0 /scratch/stefan/7769667/working/building/REAL300000086112 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/118 `/scratch/stefan/7769667/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC(CC)CC1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300000086112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086112 none CCC(=NNC(CC)CC1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [148, 80, 80, 32, 7, 2, 7, 11, 1, 1, 1, 1, 1, 1, 1, 1, 80, 106, 106, 148, 148, 148, 148, 148, 32, 7, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1] 157 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 640 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086112 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086112 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086112/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086112 Building REAL300000086113 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086113' /scratch/stefan/7769667/working/building/REAL300000086113 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086113 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086113/0 /scratch/stefan/7769667/working/building/REAL300000086113 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/119 `/scratch/stefan/7769667/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC2=CC(Br)=CC=C2O1)C(=O)[O-]) `REAL300000086113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086113 none CCC(NN=CC1=CC2=CC(Br)=CC=C2O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 35, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 37, 37, 51, 51, 51, 51, 51, 35, 22, 6, 1, 1, 1, 1] 51 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086113 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086113 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086113/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086113 Building REAL300000086114 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086114' /scratch/stefan/7769667/working/building/REAL300000086114 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086114 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086114/0 /scratch/stefan/7769667/working/building/REAL300000086114 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/120 `/scratch/stefan/7769667/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCOC2=CC(F)=C(Cl)C=C21)C(=O)[O-]) `REAL300000086114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086114 none CCC(NN=C1CCOC2=CC(F)=C(Cl)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 12, 1, 1, 1, 15, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 18, 18, 23, 23, 23, 23, 23, 15, 7, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31] set([0, 1, 2, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 105 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086114 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086114 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086114/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086114 Building REAL300000086115 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086115' /scratch/stefan/7769667/working/building/REAL300000086115 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086115 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086115/0 /scratch/stefan/7769667/working/building/REAL300000086115 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/121 `/scratch/stefan/7769667/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C(C)C1=CC=C(CC(C)C)C=C1)C(=O)[O-]) `REAL300000086115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086115 none CCC(NN=C(C)C(C)C1=CC=C(CC(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 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: [16, 14, 12, 6, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 14, 14, 14, 16, 16, 16, 16, 16, 14, 12, 6, 6, 6, 3, 3, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 26 rigid atoms, others: [36, 37, 7, 9, 10, 11, 12, 13, 47, 48, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086115 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086115 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086115/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086115 Building REAL300000086116 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086116' /scratch/stefan/7769667/working/building/REAL300000086116 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086116 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086116/0 /scratch/stefan/7769667/working/building/REAL300000086116 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/122 `/scratch/stefan/7769667/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN=CC(Br)=C1C)C(=O)[O-]) `REAL300000086116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086116 none CCC(NN=CC1=CN=CC(Br)=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 17, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [70, 54, 40, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 57, 57, 70, 70, 70, 70, 70, 54, 40, 12, 1, 1, 2, 2, 2] 71 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 278 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086116 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086116 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086116/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086116 Building REAL300000086117 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086117' /scratch/stefan/7769667/working/building/REAL300000086117 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086117 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086117/0 /scratch/stefan/7769667/working/building/REAL300000086117 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/123 `/scratch/stefan/7769667/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCN(C2=CC=C([N+](=O)[O-])N=C2)CC1)C(=O)[O-]) `REAL300000086117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086117 none CCC(NN=C1CCN(C2=CC=C([N+](=O)[O-])N=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 5, 8, 1, 1, 1, 1, 8, 11, 11, 8, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [42, 26, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 10, 10, 11, 11, 11, 11, 1, 1, 26, 34, 34, 42, 42, 42, 42, 42, 26, 8, 1, 1, 1, 1, 11, 11, 11, 1, 1, 1, 1] 99 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 39, 40, 18, 19, 38, 37, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36]) total number of confs: 226 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086117 none CCC(NN=C1CCN(C2=CC=C([N+](=O)[O-])N=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 5, 8, 1, 1, 1, 1, 8, 11, 11, 8, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 87, 51, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 11, 11, 87, 95, 95, 99, 99, 99, 99, 99, 87, 51, 11, 11, 11, 11, 1, 1, 1, 11, 11, 11, 11] 99 rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 394 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086117 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086117 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086117/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086117 Building REAL300000086118 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086118' /scratch/stefan/7769667/working/building/REAL300000086118 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086118 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086118/0 /scratch/stefan/7769667/working/building/REAL300000086118 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/124 `/scratch/stefan/7769667/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CCC(F)(F)F)CCC(F)(F)F)C(=O)[O-]) `REAL300000086118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086118 none CCC(NN=C(CCC(F)(F)F)CCC(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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, 5, 8, 8, 1, 5, 5, 5, 15, 15, 15, 5, 5, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 8, 9, 9, 9, 9, 11, 12, 12, 12, 12, 12, 12, 12, 11, 4, 2, 2, 2, 2, 8, 8, 9, 9] 31 rigid atoms, others: [12, 3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 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: 88 number of broken/clashed sets: 13 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086118 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086118 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086118/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086118 Building REAL300000086119 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086119' /scratch/stefan/7769667/working/building/REAL300000086119 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086119 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086119/0 /scratch/stefan/7769667/working/building/REAL300000086119 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/125 `/scratch/stefan/7769667/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(OC(C)C2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300000086119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086119 none CCC(NN=C(C)C1=CC=C(OC(C)C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', '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, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens 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, 46, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 11, 24, 24, 29, 29, 24, 29, 29, 1, 1, 46, 64, 64, 66, 66, 66, 66, 66, 46, 24, 6, 6, 6, 1, 1, 24, 24, 24, 24, 29, 29, 24, 29, 29, 1, 1] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 46, 47, 20, 21] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 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: 450 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086119 none CCC(NN=C(C)C1=CC=C(OC(C)C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', '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, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 156, 85, 85, 29, 85, 14, 29, 29, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 29, 29, 197, 201, 201, 201, 201, 201, 201, 201, 197, 156, 85, 85, 85, 29, 29, 3, 3, 3, 3, 1, 1, 1, 1, 1, 29, 29] 201 rigid atoms, others: [41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) total number of confs: 771 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086119 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086119 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086119/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086119 Building REAL300000086120 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086120' /scratch/stefan/7769667/working/building/REAL300000086120 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086120 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086120/0 /scratch/stefan/7769667/working/building/REAL300000086120 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/126 `/scratch/stefan/7769667/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CN=CC(Br)=C1)C(=O)[O-]) `REAL300000086120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086120 none CCC(NN=C(C)C1=CN=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 80, 45, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 80, 82, 82, 100, 100, 100, 100, 100, 80, 45, 12, 12, 12, 1, 1, 1] 100 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 413 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086120 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086120 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086120/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086120 Building REAL300000086121 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086121' /scratch/stefan/7769667/working/building/REAL300000086121 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086121 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086121/0 /scratch/stefan/7769667/working/building/REAL300000086121 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/127 `/scratch/stefan/7769667/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCN(CC2=CC=C(OC)C=C2)C1=O)C(=O)[O-]) `REAL300000086121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086121 none CCC(NN=C1CCN(CC2=CC=C(OC)C=C2)C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 2, 2, 7, 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: [29, 18, 3, 1, 1, 1, 1, 1, 1, 1, 9, 13, 13, 9, 13, 24, 13, 13, 1, 1, 18, 24, 24, 29, 29, 29, 29, 29, 18, 3, 1, 1, 1, 1, 9, 9, 13, 13, 25, 25, 25, 13, 13] 168 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 18, 19, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086121 none CCC(NN=C1CCN(CC2=CC=C(OC)C=C2)C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 2, 2, 7, 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: [151, 99, 35, 13, 13, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 2, 1, 1, 13, 13, 99, 128, 128, 151, 151, 151, 151, 151, 99, 35, 13, 13, 13, 13, 3, 3, 1, 1, 3, 3, 3, 1, 1] 168 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 16, 17, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 780 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086121 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086121 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086121/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086121 Building REAL300000086122 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086122' /scratch/stefan/7769667/working/building/REAL300000086122 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086122 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086122/0 /scratch/stefan/7769667/working/building/REAL300000086122 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/128 `/scratch/stefan/7769667/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C2CCN(C(=O)OC(C)(C)C)CC2=C1)C(=O)[O-]) `REAL300000086122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086122 none CCC(NN=CC1=CC=C2CCN(C(=O)OC(C)(C)C)CC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 68, 37, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 20, 20, 20, 1, 1, 1, 68, 83, 83, 90, 90, 90, 90, 90, 68, 37, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 49, 50, 51, 20, 21, 22, 39, 38, 37] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 488 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086122 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086122 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086122/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086122 Building REAL300000086123 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086123' /scratch/stefan/7769667/working/building/REAL300000086123 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086123 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086123/0 /scratch/stefan/7769667/working/building/REAL300000086123 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/129 `/scratch/stefan/7769667/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(OC2=CC=C(F)C=C2)N=C1)C(=O)[O-]) `REAL300000086123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086123 none CCC(NN=CC1=CC=C(OC2=CC=C(F)C=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [96, 65, 29, 6, 6, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 1, 1, 65, 88, 88, 96, 96, 96, 96, 96, 65, 29, 6, 1, 1, 17, 17, 17, 17, 1] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 37, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 528 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086123 none CCC(NN=CC1=CC=C(OC2=CC=C(F)C=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [201, 189, 125, 68, 68, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 189, 192, 192, 201, 201, 201, 201, 201, 189, 125, 68, 17, 17, 1, 1, 1, 1, 17] 201 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 768 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086123 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086123 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086123/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086123 Building REAL300000086124 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086124' /scratch/stefan/7769667/working/building/REAL300000086124 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086124 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086124/0 /scratch/stefan/7769667/working/building/REAL300000086124 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/130 `/scratch/stefan/7769667/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN=C(C2=CC=CC(Cl)=C2)S1)C(=O)[O-]) `REAL300000086124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086124 none CCC(NN=CC1=CN=C(C2=CC=CC(Cl)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [14, 11, 8, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 5, 1, 11, 11, 11, 14, 14, 14, 14, 14, 11, 8, 4, 1, 5, 5, 2, 5] 20 rigid atoms, others: [5, 6, 7, 8, 9, 10, 17, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086124 none CCC(NN=CC1=CN=C(C2=CC=CC(Cl)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 18, 17, 11, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 18, 18, 18, 20, 20, 20, 20, 20, 18, 17, 11, 5, 1, 1, 1, 1] 20 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086124 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086124 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086124/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086124 Building REAL300000086125 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086125' /scratch/stefan/7769667/working/building/REAL300000086125 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086125 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086125/0 /scratch/stefan/7769667/working/building/REAL300000086125 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/131 `/scratch/stefan/7769667/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=NN(C)C(C2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300000086125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086125 none CCC(NN=C(C)C1=NN(C)C(C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 1, 9, 9, 9, 12, 12, 12, 12, 12, 9, 7, 4, 4, 4, 2, 2, 2, 4, 4, 3, 4, 4, 1] 12 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 40, 18] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 59 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086125 none CCC(NN=C(C)C1=NN(C)C(C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 9, 7, 7, 4, 7, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 12, 12, 12, 12, 12, 11, 9, 7, 7, 7, 4, 4, 4, 1, 1, 1, 1, 1, 4] 12 rigid atoms, others: [35, 36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40]) total number of confs: 38 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086125 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086125 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086125/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086125 Building REAL300000086126 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086126' /scratch/stefan/7769667/working/building/REAL300000086126 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086126 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086126/0 /scratch/stefan/7769667/working/building/REAL300000086126 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/132 `/scratch/stefan/7769667/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC2=CC(OC)=C(OC)C=C2C=C1)C(=O)[O-]) `REAL300000086126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086126 none CCC(NN=C(C)C1=CC2=CC(OC)=C(OC)C=C2C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', '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', '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, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [149, 112, 57, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 1, 1, 1, 112, 136, 136, 149, 149, 149, 149, 149, 112, 57, 12, 12, 12, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1] 201 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 12, 14, 15, 17, 18, 19, 20, 43, 44, 42] set([0, 1, 2, 3, 4, 6, 13, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 714 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086126 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086126 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086126/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086126 Building REAL300000086127 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086127' /scratch/stefan/7769667/working/building/REAL300000086127 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086127 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086127/0 /scratch/stefan/7769667/working/building/REAL300000086127 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/133 `/scratch/stefan/7769667/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Cl)=C(OC(C)C)C=C1Cl)C(=O)[O-]) `REAL300000086127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086127 none CCC(NN=CC1=CC(Cl)=C(OC(C)C)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.2', 'O.co2', 'O.co2', 'H', '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, 16, 1, 12, 5, 5, 5, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [113, 76, 42, 10, 10, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 1, 1, 1, 76, 101, 101, 113, 113, 113, 113, 113, 76, 42, 10, 1, 19, 19, 19, 19, 19, 19, 19, 1] 192 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 29, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 630 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086127 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086127 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086127/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086127 Building REAL300000086128 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086128' /scratch/stefan/7769667/working/building/REAL300000086128 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086128 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086128/0 /scratch/stefan/7769667/working/building/REAL300000086128 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/134 `/scratch/stefan/7769667/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(NS(=O)(=O)C2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300000086128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086128 none CCC(NN=C(C)C1=CC=C(NS(=O)(=O)C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', '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', '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, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens 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, 52, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 52, 71, 71, 79, 79, 79, 79, 79, 52, 25, 7, 7, 7, 1, 1, 7, 17, 17, 17, 17, 17, 1, 1] 201 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 44, 45, 21, 22, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 478 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086128 none CCC(NN=C(C)C1=CC=C(NS(=O)(=O)C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', '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', '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, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 140, 61, 61, 10, 61, 9, 17, 17, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 17, 17, 191, 201, 201, 201, 201, 201, 201, 201, 191, 140, 59, 61, 61, 17, 17, 5, 1, 1, 1, 1, 1, 17, 17] 201 rigid atoms, others: [39, 40, 41, 42, 43, 12, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45]) total number of confs: 810 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086128 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086128/1 /scratch/stefan/7769667/working/building/REAL300000086128 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/135 `/scratch/stefan/7769667/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300000086128.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086128 none CCC(NN=C(C)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 55, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 55, 82, 82, 90, 90, 90, 90, 90, 55, 28, 7, 7, 7, 1, 1, 18, 18, 18, 18, 18, 1, 1] 201 rigid atoms, others: [43, 36, 5, 7, 8, 9, 10, 11, 44, 21, 22, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42]) total number of confs: 557 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086128 none CCC(NN=C(C)C1=CC=C([N-]S(=O)(=O)C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 193, 147, 67, 67, 9, 67, 9, 18, 18, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 18, 18, 193, 201, 201, 201, 201, 201, 201, 201, 193, 147, 65, 67, 67, 18, 18, 1, 1, 1, 1, 1, 18, 18] 201 rigid atoms, others: [38, 39, 40, 41, 42, 12, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44]) total number of confs: 771 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086128 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086128 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086128/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086128/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086128 Building REAL300000086129 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086129' /scratch/stefan/7769667/working/building/REAL300000086129 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300000086129 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086129/0 /scratch/stefan/7769667/working/building/REAL300000086129 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/136 `/scratch/stefan/7769667/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCN(C)C(C2=CC=C(Br)C=C2)C1)C(=O)[O-]) `REAL300000086129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086129 none CCC(NN=C1CCN(C)C(C2=CC=C(Br)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 10, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 11, 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, 4, 7, 7, 7, 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, 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: [34, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 2, 3, 3, 1, 20, 26, 26, 34, 34, 34, 34, 34, 20, 7, 1, 1, 1, 1, 2, 2, 2, 1, 3, 3, 3, 3, 1, 1] 35 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 42, 41, 36, 29, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 37, 38, 39, 40]) total number of confs: 180 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086129 none CCC(NN=C1CCN(C)C(C2=CC=C(Br)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 10, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 11, 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, 4, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 30, 12, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 30, 34, 34, 35, 35, 35, 35, 35, 30, 12, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 35 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 153 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086129 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086129/1 /scratch/stefan/7769667/working/building/REAL300000086129 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/137 `/scratch/stefan/7769667/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC[N@H+](C)C(C2=CC=C(Br)C=C2)C1)C(=O)[O-]) `REAL300000086129.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086129 none CCC(NN=C1CC[N@H+](C)C(C2=CC=C(Br)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 9, 6, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 11, 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, 4, 7, 7, 7, 7, 1, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 11, 12, 12, 15, 15, 15, 15, 15, 11, 5, 1, 1, 1, 1, 2, 2, 2, 1, 3, 3, 3, 3, 1, 1] 15 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 43, 19, 42, 37, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 79 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086129 none CCC(NN=C1CC[N@H+](C)C(C2=CC=C(Br)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 9, 6, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 11, 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, 4, 7, 7, 7, 7, 1, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 8, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 14, 15, 15, 15, 15, 15, 15, 15, 14, 8, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 15 rigid atoms, others: [38, 39, 40, 41, 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, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 64 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086129 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `2' /scratch/stefan/7769667/working/building/REAL300000086129/2 /scratch/stefan/7769667/working/building/REAL300000086129 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 2 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/138 `/scratch/stefan/7769667/working/3D/138' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC[N@@H+](C)C(C2=CC=C(Br)C=C2)C1)C(=O)[O-]) `REAL300000086129.mol2' -> `2.mol2' `temp.mol2' -> `REAL300000086129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086129/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086129 none CCC(NN=C1CC[N@@H+](C)C(C2=CC=C(Br)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 9, 6, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 11, 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, 4, 7, 7, 7, 7, 1, 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 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 6, 7, 7, 8, 8, 8, 8, 8, 6, 3, 1, 1, 1, 1, 2, 2, 2, 1, 3, 3, 3, 3, 1, 1] 8 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 43, 19, 42, 37, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 51 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086129 none CCC(NN=C1CC[N@@H+](C)C(C2=CC=C(Br)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 9, 6, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 11, 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, 4, 7, 7, 7, 7, 1, 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 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 8, 8, 8, 8, 8, 8, 8, 7, 5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 8 rigid atoms, others: [38, 39, 40, 41, 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, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 37 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086129 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086129 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 2: /scratch/stefan/7769667/working/building/REAL300000086129/2.* 0: /scratch/stefan/7769667/working/building/REAL300000086129/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086129/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086129 Building REAL300000086130 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086130' /scratch/stefan/7769667/working/building/REAL300000086130 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086130 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086130/0 /scratch/stefan/7769667/working/building/REAL300000086130 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/139 `/scratch/stefan/7769667/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCN(C(=O)OC(C)(C)C)CC(C)(C)C1)C(=O)[O-]) `REAL300000086130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086130 none CCC(NN=C1CCN(C(=O)OC(C)(C)C)CC(C)(C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [31, 22, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 1, 1, 1, 1, 1, 22, 29, 29, 31, 31, 31, 31, 31, 22, 7, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 53 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 44, 45, 16, 17, 18, 19, 20, 53, 52, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086130 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086130 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086130/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086130 Building REAL300000086131 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086131' /scratch/stefan/7769667/working/building/REAL300000086131 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086131 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086131/0 /scratch/stefan/7769667/working/building/REAL300000086131 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/140 `/scratch/stefan/7769667/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC(F)=C(Br)C=C1F)C(=O)[O-]) `REAL300000086131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086131 none CCC(NN=C(C)C1=CC(F)=C(Br)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 15, 1, 17, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 62, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 65, 65, 82, 82, 82, 82, 82, 62, 37, 11, 11, 11, 1, 1] 82 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 349 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086131 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086131 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086131/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086131 Building REAL300000086132 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086132' /scratch/stefan/7769667/working/building/REAL300000086132 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086132 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086132/0 /scratch/stefan/7769667/working/building/REAL300000086132 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/141 `/scratch/stefan/7769667/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1(C(C)(C)C)CC[N@H+](CC2=CC=CC=C2)C1)C(=O)[O-]) `REAL300000086132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086132 none CCC(NN=CC1(C(C)(C)C)CC[N@H+](CC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 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, 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, 17, 14, 6, 6, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 17, 21, 21, 27, 27, 27, 27, 27, 17, 14, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 1, 1] 37 rigid atoms, others: [43, 5, 6, 7, 54, 44, 11, 12, 13, 46, 45, 14, 22, 55, 15] set([0, 1, 2, 3, 4, 8, 9, 10, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 145 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086132 none CCC(NN=CC1(C(C)(C)C)CC[N@H+](CC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 32, 29, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 1, 1, 1, 1, 1, 1, 1, 7, 32, 37, 37, 37, 37, 37, 37, 37, 32, 29, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 7, 7] 37 rigid atoms, others: [51, 49, 50, 15, 16, 17, 18, 19, 20, 21, 52, 53] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55]) total number of confs: 155 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086132 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086132/1 /scratch/stefan/7769667/working/building/REAL300000086132 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/142 `/scratch/stefan/7769667/working/3D/142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1(C(C)(C)C)CC[N@@H+](CC2=CC=CC=C2)C1)C(=O)[O-]) `REAL300000086132.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086132 none CCC(NN=CC1(C(C)(C)C)CC[N@@H+](CC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [58, 42, 22, 7, 7, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 7, 10, 10, 7, 10, 10, 1, 42, 53, 53, 58, 58, 58, 58, 58, 42, 22, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 1, 1] 100 rigid atoms, others: [43, 5, 6, 7, 54, 44, 11, 12, 13, 46, 45, 14, 22, 55, 15] set([0, 1, 2, 3, 4, 8, 9, 10, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 336 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086132 none CCC(NN=CC1(C(C)(C)C)CC[N@@H+](CC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 92, 69, 29, 29, 10, 10, 10, 10, 10, 10, 10, 10, 4, 10, 1, 1, 1, 1, 1, 1, 1, 10, 92, 100, 100, 100, 100, 100, 100, 100, 92, 69, 29, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 10, 10] 100 rigid atoms, others: [51, 49, 50, 15, 16, 17, 18, 19, 20, 21, 52, 53] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55]) total number of confs: 416 number of broken/clashed sets: 100 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086132 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086132 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086132/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086132/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086132 Building REAL300000086133 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086133' /scratch/stefan/7769667/working/building/REAL300000086133 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086133 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086133/0 /scratch/stefan/7769667/working/building/REAL300000086133 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/143 `/scratch/stefan/7769667/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC2=C1CCN(C(=O)OC(C)(C)C)C2)C(=O)[O-]) `REAL300000086133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086133 none CCC(NN=CC1=CC=CC2=C1CCN(C(=O)OC(C)(C)C)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 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: [71, 61, 39, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 16, 16, 16, 1, 61, 66, 66, 71, 71, 71, 71, 71, 61, 39, 11, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1] 144 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 50, 51, 22, 39, 38, 37] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086133 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086133 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086133/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086133 Building REAL300000086134 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086134' /scratch/stefan/7769667/working/building/REAL300000086134 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086134 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086134/0 /scratch/stefan/7769667/working/building/REAL300000086134 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/144 `/scratch/stefan/7769667/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C(=O)OC)=C2CCCCN12)C(=O)[O-]) `REAL300000086134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086134 none CCC(NN=CC1=CC(C(=O)OC)=C2CCCCN12)C(=O)[O-] 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', 'O.2', 'O.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 11, 12, 5, 1, 5, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 5, 3, 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] 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, 39, 20, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 1, 1, 1, 1, 1, 1, 39, 48, 48, 53, 53, 53, 53, 53, 39, 20, 6, 1, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1] 85 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 39, 13, 14, 15, 16, 17, 18, 41, 40, 38, 30, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086134 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086134 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086134/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086134 Building REAL300000086135 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086135' /scratch/stefan/7769667/working/building/REAL300000086135 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086135 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086135/0 /scratch/stefan/7769667/working/building/REAL300000086135 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/145 `/scratch/stefan/7769667/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC(CC)CC1=CC=C(C(F)(F)F)C=C1)C(=O)[O-]) `REAL300000086135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086135 none CCC(=NNC(CC)CC1=CC=C(C(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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, 5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 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 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [155, 90, 90, 33, 7, 2, 7, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 90, 117, 117, 155, 155, 155, 155, 155, 33, 7, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1] 162 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 631 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086135 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086135 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086135/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086135 Building REAL300000086136 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086136' /scratch/stefan/7769667/working/building/REAL300000086136 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086136 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086136/0 /scratch/stefan/7769667/working/building/REAL300000086136 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/146 `/scratch/stefan/7769667/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC2=CC=C(I)C=C21)C(=O)[O-]) `REAL300000086136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086136 none CCC(NN=C1CCC2=CC=C(I)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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, 5, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 14, 14, 14, 14, 14, 9, 5, 1, 1, 1, 1, 1, 1, 1] 14 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 59 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086136 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086136 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086136/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086136 Building REAL300000086137 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086137' /scratch/stefan/7769667/working/building/REAL300000086137 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086137 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086137/0 /scratch/stefan/7769667/working/building/REAL300000086137 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/147 `/scratch/stefan/7769667/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(OC)=CC(C(F)(F)F)=C1)C(=O)[O-]) `REAL300000086137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086137 none CCC(NN=CC1=CC(OC)=CC(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 5, 5, 8, 8, 1, 1, 1, 1, 12, 5, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [82, 68, 40, 11, 11, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 68, 74, 74, 82, 82, 82, 82, 82, 68, 40, 11, 1, 3, 3, 3, 1, 1] 125 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 32, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 356 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086137 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086137 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086137/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086137 Building REAL300000086138 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086138' /scratch/stefan/7769667/working/building/REAL300000086138 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086138 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086138/0 /scratch/stefan/7769667/working/building/REAL300000086138 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/148 `/scratch/stefan/7769667/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=C(Cl)C=C(CNN=C(CC)C(=O)[O-])C=C1OC) `REAL300000086138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086138 none C=CCOC1=C(Cl)C=C(CNN=C(CC)C(=O)[O-])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.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 5, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens 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, 15, 2, 1, 1, 1, 1, 1, 1, 1, 2, 9, 22, 22, 72, 22, 33, 33, 1, 1, 1, 3, 49, 49, 49, 15, 15, 1, 2, 2, 9, 72, 72, 72, 72, 72, 1, 3, 3, 3] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 36, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 431 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086138 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086138 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086138/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086138 Building REAL300000086139 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086139' /scratch/stefan/7769667/working/building/REAL300000086139 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086139 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086139/0 /scratch/stefan/7769667/working/building/REAL300000086139 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/149 `/scratch/stefan/7769667/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Cl)=CC=C1I)C(=O)[O-]) `REAL300000086139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086139 none CCC(NN=CC1=CC(Cl)=CC=C1I)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 18, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [57, 41, 31, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 46, 46, 57, 57, 57, 57, 57, 41, 31, 10, 1, 1, 1] 59 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086139 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086139 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086139/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086139 Building REAL300000086140 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086140' /scratch/stefan/7769667/working/building/REAL300000086140 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086140 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086140/0 /scratch/stefan/7769667/working/building/REAL300000086140 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/150 `/scratch/stefan/7769667/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(Br)C=C1O)C(=O)[O-]) `REAL300000086140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086140 none CCC(NN=CC1=CC=C(Br)C=C1O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 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: [35, 27, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 35, 35, 35, 35, 35, 27, 18, 5, 1, 1, 1, 2] 70 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28]) total number of confs: 135 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086140 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086140 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086140/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086140 Building REAL300000086141 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086141' /scratch/stefan/7769667/working/building/REAL300000086141 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086141 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086141/0 /scratch/stefan/7769667/working/building/REAL300000086141 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/151 `/scratch/stefan/7769667/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(C)N=C1CN1C(=O)C2=CC=CC=C2C1=O)C(=O)[O-]) `REAL300000086141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086141 none CCC(NN=CC1=CN(C)N=C1CN1C(=O)C2=CC=CC=C2C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 5, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [85, 59, 26, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 59, 73, 73, 85, 85, 85, 85, 85, 59, 26, 10, 1, 2, 2, 2, 7, 7, 16, 16, 16, 16] 139 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 12] 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, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 459 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086141 none CCC(NN=CC1=CN(C)N=C1CN1C(=O)C2=CC=CC=C2C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 5, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 31, 24, 17, 17, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 32, 32, 32, 32, 32, 32, 32, 31, 24, 17, 13, 13, 13, 13, 6, 6, 1, 1, 1, 1] 32 rigid atoms, others: [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, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086141 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086141 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086141/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086141 Building REAL300000086142 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086142' /scratch/stefan/7769667/working/building/REAL300000086142 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086142 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086142/0 /scratch/stefan/7769667/working/building/REAL300000086142 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/152 `/scratch/stefan/7769667/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1OCC1=CC=C(F)C=C1F)C(=O)[O-]) `REAL300000086142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086142 none CCC(NN=CC1=CC=CC=C1OCC1=CC=C(F)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'F', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', '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, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 18, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 31, 102, 102, 31, 102, 102, 102, 102, 18, 28, 28, 32, 32, 32, 32, 32, 18, 7, 4, 1, 1, 1, 1, 31, 31, 102, 102, 102] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12] 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, 37, 38, 39, 40, 41]) total number of confs: 586 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086142 none CCC(NN=CC1=CC=CC=C1OCC1=CC=C(F)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'F', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', '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, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 157, 137, 118, 118, 102, 102, 102, 102, 102, 102, 47, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 157, 201, 201, 201, 201, 201, 201, 201, 157, 137, 118, 102, 102, 102, 102, 7, 7, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 838 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086142 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086142 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086142/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086142 Building REAL300000086143 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086143' /scratch/stefan/7769667/working/building/REAL300000086143 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086143 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086143/0 /scratch/stefan/7769667/working/building/REAL300000086143 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/153 `/scratch/stefan/7769667/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C([N+](=O)[O-])C=C1Br)C(=O)[O-]) `REAL300000086143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086143 none CCC(NN=C(C)C1=CC=C([N+](=O)[O-])C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', '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, 11, 11, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 43, 27, 8, 8, 1, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 43, 46, 46, 56, 56, 56, 56, 56, 43, 27, 8, 8, 8, 1, 1, 1] 56 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 239 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086143 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086143 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086143/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086143 Building REAL300000086144 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086144' /scratch/stefan/7769667/working/building/REAL300000086144 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086144 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086144/0 /scratch/stefan/7769667/working/building/REAL300000086144 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/154 `/scratch/stefan/7769667/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=NN1CCC1=CC=CC=C1)C(=O)[O-]) `REAL300000086144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086144 none CCC(NN=CC1=CC=NN1CCC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 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: [48, 30, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 11, 21, 21, 12, 21, 21, 30, 40, 40, 48, 48, 48, 48, 48, 30, 13, 4, 1, 1, 5, 5, 11, 11, 21, 21, 21, 21, 21] 117 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 334 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086144 none CCC(NN=CC1=CC=NN1CCC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [117, 94, 68, 44, 44, 21, 21, 21, 21, 21, 7, 3, 1, 1, 1, 1, 1, 1, 1, 94, 105, 105, 117, 117, 117, 117, 117, 94, 68, 44, 21, 21, 7, 7, 3, 3, 1, 1, 1, 1, 1] 117 rigid atoms, others: [36, 37, 38, 39, 40, 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, 35]) total number of confs: 522 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086144 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086144 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086144/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086144 Building REAL300000086145 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086145' /scratch/stefan/7769667/working/building/REAL300000086145 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086145 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086145/0 /scratch/stefan/7769667/working/building/REAL300000086145 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/155 `/scratch/stefan/7769667/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C(F)(F)F)=C(Br)C=C1F)C(=O)[O-]) `REAL300000086145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086145 none CCC(NN=CC1=CC(C(F)(F)F)=C(Br)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 17, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 39, 24, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 40, 40, 43, 43, 43, 43, 43, 39, 24, 9, 1, 1] 43 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086145 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086145 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086145/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086145 Building REAL300000086146 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086146' /scratch/stefan/7769667/working/building/REAL300000086146 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086146 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086146/0 /scratch/stefan/7769667/working/building/REAL300000086146 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/156 `/scratch/stefan/7769667/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(F)=C1OCC(F)(F)F)C(=O)[O-]) `REAL300000086146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086146 none CCC(NN=CC1=CC=CC(F)=C1OCC(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.2', 'O.co2', 'O.co2', '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, 15, 1, 12, 5, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 92, 41, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 92, 122, 122, 136, 136, 136, 136, 136, 92, 41, 13, 1, 1, 1, 12, 12] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 742 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086146 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086146 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086146/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086146 Building REAL300000086147 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086147' /scratch/stefan/7769667/working/building/REAL300000086147 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086147 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086147/0 /scratch/stefan/7769667/working/building/REAL300000086147 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/157 `/scratch/stefan/7769667/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(C(F)(C(F)(F)F)C(F)(F)F)C=C1)C(=O)[O-]) `REAL300000086147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086147 none CCC(NN=CC1=CC=C(C(F)(C(F)(F)F)C(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 15, 5, 15, 15, 15, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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] 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, 36, 21, 6, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 36, 43, 43, 47, 47, 47, 47, 47, 36, 21, 6, 1, 1, 1, 1] 79 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 20, 21] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 238 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086147 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086147 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086147/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086147 Building REAL300000086148 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086148' /scratch/stefan/7769667/working/building/REAL300000086148 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086148 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086148/0 /scratch/stefan/7769667/working/building/REAL300000086148 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/158 `/scratch/stefan/7769667/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(O)C=CC=C1OC(F)(F)F)C(=O)[O-]) `REAL300000086148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086148 none CCC(NN=CC1=C(O)C=CC=C1OC(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 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: [127, 88, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 88, 116, 116, 127, 127, 127, 127, 127, 88, 50, 13, 2, 1, 1, 1] 402 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 697 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086148 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086148 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086148/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086148 Building REAL300000086149 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086149' /scratch/stefan/7769667/working/building/REAL300000086149 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086149 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086149/0 /scratch/stefan/7769667/working/building/REAL300000086149 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/159 `/scratch/stefan/7769667/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=C(Br)N1)C(=O)[O-]) `REAL300000086149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086149 none CCC(NN=CC1=CC(Br)=C(Br)N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'Br', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 17, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 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: [53, 40, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 40, 43, 43, 53, 53, 53, 53, 53, 40, 25, 6, 1, 1] 55 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 24, 25] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086149 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086149 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086149/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086149 Building REAL300000086150 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086150' /scratch/stefan/7769667/working/building/REAL300000086150 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086150 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086150/0 /scratch/stefan/7769667/working/building/REAL300000086150 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/160 `/scratch/stefan/7769667/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C(=O)NC2=CC(Br)=C(OC)C=C21)C(=O)[O-]) `REAL300000086150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086150 none CCC(NN=C1C(=O)NC2=CC(Br)=C(OC)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 17, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 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] 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: [30, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 21, 26, 26, 30, 30, 30, 30, 30, 21, 6, 1, 1, 4, 4, 4, 1] 32 rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 28, 29] set([0, 1, 2, 32, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086150 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086150 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086150/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086150 Building REAL300000086151 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086151' /scratch/stefan/7769667/working/building/REAL300000086151 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086151 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086151/0 /scratch/stefan/7769667/working/building/REAL300000086151 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/161 `/scratch/stefan/7769667/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C)N(C2=CC=C(OC)C(OC)=C2)C(C)=C1)C(=O)[O-]) `REAL300000086151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086151 none CCC(NN=CC1=C(C)N(C2=CC=C(OC)C(OC)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 5, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 5, 1, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 30, 23, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 17, 7, 7, 17, 7, 1, 1, 1, 30, 35, 35, 45, 45, 45, 45, 45, 30, 22, 6, 2, 2, 2, 7, 7, 17, 17, 17, 17, 17, 17, 7, 2, 2, 2, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 49, 20, 21, 22] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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, 47, 48]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086151 none CCC(NN=CC1=C(C)N(C2=CC=C(OC)C(OC)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 5, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 5, 1, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 88, 76, 33, 33, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 7, 7, 7, 88, 103, 103, 132, 132, 132, 132, 132, 88, 76, 33, 7, 7, 7, 1, 1, 4, 4, 4, 4, 4, 4, 1, 7, 7, 7, 7] 201 rigid atoms, others: [37, 38, 9, 10, 11, 12, 13, 14, 45, 16, 17, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 608 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086151 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086151 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086151/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086151 Building REAL300000086152 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086152' /scratch/stefan/7769667/working/building/REAL300000086152 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086152 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086152/0 /scratch/stefan/7769667/working/building/REAL300000086152 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/162 `/scratch/stefan/7769667/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC(C(=O)OC)CN(C(=O)OC(C)(C)C)C1)C(=O)[O-]) `REAL300000086152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086152 none CCC(NN=C1CC(C(=O)OC)CN(C(=O)OC(C)(C)C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 1, 11, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 6, 6, 17, 18, 18, 18, 1, 19, 30, 30, 33, 33, 33, 33, 33, 19, 8, 1, 1, 1, 3, 3, 3, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 39, 12, 13, 14, 49, 50, 21, 38] set([0, 1, 2, 9, 10, 11, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 247 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086152 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086152 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086152/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086152 Building REAL300000086153 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086153' /scratch/stefan/7769667/working/building/REAL300000086153 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086153 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086153/0 /scratch/stefan/7769667/working/building/REAL300000086153 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/163 `/scratch/stefan/7769667/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(Br)C(Cl)=C1)C(=O)[O-]) `REAL300000086153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086153 none CCC(NN=C(C)C1=CC=C(Br)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 67, 42, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 67, 72, 72, 91, 91, 91, 91, 91, 67, 42, 10, 10, 10, 1, 1, 1] 91 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 372 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086153 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086153 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086153/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086153 Building REAL300000086154 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086154' /scratch/stefan/7769667/working/building/REAL300000086154 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086154 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086154/0 /scratch/stefan/7769667/working/building/REAL300000086154 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/164 `/scratch/stefan/7769667/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C(F)(F)F)N=C2CCCCN21)C(=O)[O-]) `REAL300000086154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086154 none CCC(NN=CC1=C(C(F)(F)F)N=C2CCCCN21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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, 5, 5, 8, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 5, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 40, 29, 9, 9, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 40, 49, 49, 53, 53, 53, 53, 53, 40, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1] 53 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 37, 30, 31] set([0, 1, 2, 3, 4, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 243 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086154 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086154 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086154/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086154 Building REAL300000086155 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086155' /scratch/stefan/7769667/working/building/REAL300000086155 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086155 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086155/0 /scratch/stefan/7769667/working/building/REAL300000086155 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/165 `/scratch/stefan/7769667/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C(=O)NC2=C1C=CC(C)=C2Br)C(=O)[O-]) `REAL300000086155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086155 none CCC(NN=C1C(=O)NC2=C1C=CC(C)=C2Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 15, 15, 18, 18, 18, 18, 18, 14, 6, 1, 1, 1, 2, 2, 2] 18 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29] set([0, 1, 2, 32, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086155 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086155 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086155/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086155 Building REAL300000086156 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086156' /scratch/stefan/7769667/working/building/REAL300000086156 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086156 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086156/0 /scratch/stefan/7769667/working/building/REAL300000086156 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/166 `/scratch/stefan/7769667/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CC1=CC=C(Br)C=C1)C1CCC1)C(=O)[O-]) `REAL300000086156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086156 none CCC(NN=C(CC1=CC=C(Br)C=C1)C1CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 7, 7] 0 hydrogens 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, 131, 75, 18, 18, 3, 1, 1, 1, 1, 1, 1, 1, 1, 18, 44, 44, 44, 131, 155, 155, 169, 169, 169, 169, 169, 131, 75, 3, 3, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 877 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086156 none CCC(NN=C(CC1=CC=C(Br)C=C1)C1CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 57, 30, 8, 8, 1, 8, 32, 44, 44, 32, 34, 44, 44, 1, 1, 1, 1, 57, 78, 78, 84, 84, 84, 84, 84, 57, 30, 32, 32, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 39, 40, 14, 15, 16, 17, 37] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 587 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086156 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086156 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086156/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086156 Building REAL300000086157 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086157' /scratch/stefan/7769667/working/building/REAL300000086157 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086157 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086157/0 /scratch/stefan/7769667/working/building/REAL300000086157 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/167 `/scratch/stefan/7769667/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(I)C=NN1C)C(=O)[O-]) `REAL300000086157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086157 none CCC(NN=CC1=C(I)C=NN1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'I', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 18, 1, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 39, 29, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 39, 41, 41, 54, 54, 54, 54, 54, 39, 29, 8, 1, 2, 2, 2] 54 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 24] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086157 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086157 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086157/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086157 Building REAL300000086158 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086158' /scratch/stefan/7769667/working/building/REAL300000086158 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086158 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086158/0 /scratch/stefan/7769667/working/building/REAL300000086158 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/168 `/scratch/stefan/7769667/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C(=O)NC2=CC=C(OC(F)(F)F)C=C21)C(=O)[O-]) `REAL300000086158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086158 none CCC(NN=C1C(=O)NC2=CC=C(OC(F)(F)F)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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, 5, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 1, 1, 14, 18, 18, 21, 21, 21, 21, 21, 14, 3, 1, 1, 1, 1] 37 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 30, 31] set([0, 1, 2, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086158 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086158 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086158/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086158 Building REAL300000086159 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086159' /scratch/stefan/7769667/working/building/REAL300000086159 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086159 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086159/0 /scratch/stefan/7769667/working/building/REAL300000086159 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/169 `/scratch/stefan/7769667/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C(=O)NC2=CC=C(F)C(Br)=C21)C(=O)[O-]) `REAL300000086159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086159 none CCC(NN=C1C(=O)NC2=CC=C(F)C(Br)=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 16, 16, 16, 16, 16, 14, 5, 1, 1, 1] 16 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29] set([0, 1, 2, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086159 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086159 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086159/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086159 Building REAL300000086160 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086160' /scratch/stefan/7769667/working/building/REAL300000086160 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086160 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086160/0 /scratch/stefan/7769667/working/building/REAL300000086160 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/170 `/scratch/stefan/7769667/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1C(=O)C(=NNC(CC)C(=O)[O-])C2=CC(C)=CC=C21) `REAL300000086160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086160 none CCCN1C(=O)C(=NNC(CC)C(=O)[O-])C2=CC(C)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 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, 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: [10, 4, 1, 1, 1, 1, 1, 1, 1, 7, 20, 33, 20, 28, 28, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 4, 4, 7, 20, 33, 33, 33, 33, 33, 1, 2, 2, 2, 1, 1] 72 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 41, 15, 16, 17, 18, 19, 20, 21, 40, 36] set([0, 1, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086160 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086160 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086160/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086160 Building REAL300000086161 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086161' /scratch/stefan/7769667/working/building/REAL300000086161 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086161 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086161/0 /scratch/stefan/7769667/working/building/REAL300000086161 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/171 `/scratch/stefan/7769667/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(OC)C=CC=C1OC(F)(F)F)C(=O)[O-]) `REAL300000086161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086161 none CCC(NN=CC1=C(OC)C=CC=C1OC(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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, 5, 5, 8, 8, 1, 1, 1, 12, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 73, 42, 13, 13, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 7, 19, 19, 19, 73, 96, 96, 100, 100, 100, 100, 100, 73, 42, 13, 4, 4, 4, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 568 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086161 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086161 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086161/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086161 Building REAL300000086162 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086162' /scratch/stefan/7769667/working/building/REAL300000086162 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086162 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086162/0 /scratch/stefan/7769667/working/building/REAL300000086162 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/172 `/scratch/stefan/7769667/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C)=C(Br)C=N1)C(=O)[O-]) `REAL300000086162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086162 none CCC(NN=CC1=CC(C)=C(Br)C=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 1, 17, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 32, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 33, 33, 41, 41, 41, 41, 41, 32, 22, 6, 1, 2, 2, 2, 1] 41 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 29] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086162 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086162 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086162/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086162 Building REAL300000086163 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086163' /scratch/stefan/7769667/working/building/REAL300000086163 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086163 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086163/0 /scratch/stefan/7769667/working/building/REAL300000086163 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/173 `/scratch/stefan/7769667/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C)=C(F)C=C1Br)C(=O)[O-]) `REAL300000086163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086163 none CCC(NN=CC1=CC(C)=C(F)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', '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, 5, 1, 15, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 50, 50, 50, 50, 50, 38, 26, 9, 1, 2, 2, 2, 1] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 30] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086163 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086163 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086163/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086163 Building REAL300000086164 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086164' /scratch/stefan/7769667/working/building/REAL300000086164 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086164 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086164/0 /scratch/stefan/7769667/working/building/REAL300000086164 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/174 `/scratch/stefan/7769667/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC2CCN(C(=O)OC(C)(C)C)C12)C(=O)[O-]) `REAL300000086164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086164 none CCC(NN=C1CCC2CCN(C(=O)OC(C)(C)C)C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 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, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 1, 24, 32, 32, 37, 37, 37, 37, 37, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1] 48 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 48, 19, 36, 38, 35, 37, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086164 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086164 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086164/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086164 Building REAL300000086165 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086165' /scratch/stefan/7769667/working/building/REAL300000086165 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086165 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086165/0 /scratch/stefan/7769667/working/building/REAL300000086165 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/175 `/scratch/stefan/7769667/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(C(=O)OC(C)(C)C)S1)C(=O)[O-]) `REAL300000086165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086165 none CCC(NN=CC1=CC=C(C(=O)OC(C)(C)C)S1)C(=O)[O-] 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', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 4, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 5, 7, 7, 7, 1, 5, 6, 6, 9, 9, 9, 9, 9, 5, 4, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8] 20 rigid atoms, others: [5, 6, 7, 8, 9, 10, 17, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086165 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086165 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086165/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086165 Building REAL300000086166 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086166' /scratch/stefan/7769667/working/building/REAL300000086166 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086166 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086166/0 /scratch/stefan/7769667/working/building/REAL300000086166 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/176 `/scratch/stefan/7769667/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(O)C=CC=C1Br)C(=O)[O-]) `REAL300000086166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086166 none CCC(NN=CC1=C(O)C=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [81, 63, 39, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 66, 66, 81, 81, 81, 81, 81, 63, 39, 11, 2, 1, 1, 1] 162 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 330 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086166 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086166 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086166/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086166 Building REAL300000086167 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086167' /scratch/stefan/7769667/working/building/REAL300000086167 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086167 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086167/0 /scratch/stefan/7769667/working/building/REAL300000086167 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/177 `/scratch/stefan/7769667/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=CC(SC(F)(F)F)=C1)C(=O)[O-]) `REAL300000086167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086167 none CCC(NN=C(C)C1=CC=CC(SC(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens 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, 50, 33, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 12, 25, 25, 25, 1, 50, 63, 63, 81, 81, 81, 81, 81, 50, 33, 10, 10, 10, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 17, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 485 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086167 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086167 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086167/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086167 Building REAL300000086168 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086168' /scratch/stefan/7769667/working/building/REAL300000086168 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086168 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086168/0 /scratch/stefan/7769667/working/building/REAL300000086168 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/178 `/scratch/stefan/7769667/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(OC)=C(Br)C=C1F)C(=O)[O-]) `REAL300000086168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086168 none CCC(NN=CC1=CC(OC)=C(Br)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 12, 5, 1, 17, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 6, 3, 3, 1, 1, 1, 1, 1, 4, 1, 1, 1, 1, 1, 9, 9, 9, 11, 11, 11, 11, 11, 9, 6, 3, 1, 4, 4, 4, 1] 11 rigid atoms, others: [5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 27, 31] set([0, 1, 2, 3, 4, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086168 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086168 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086168/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086168 Building REAL300000086169 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086169' /scratch/stefan/7769667/working/building/REAL300000086169 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086169 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086169/0 /scratch/stefan/7769667/working/building/REAL300000086169 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/179 `/scratch/stefan/7769667/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(Br)=C1Cl)C(=O)[O-]) `REAL300000086169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086169 none CCC(NN=CC1=CC=CC(Br)=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 35, 24, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 36, 36, 46, 46, 46, 46, 46, 35, 24, 8, 1, 1, 1] 46 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086169 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086169 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086169/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086169 Building REAL300000086170 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086170' /scratch/stefan/7769667/working/building/REAL300000086170 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086170 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086170/0 /scratch/stefan/7769667/working/building/REAL300000086170 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/180 `/scratch/stefan/7769667/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(NC(=O)OC(C)(C)C)N=N1)C(=O)[O-]) `REAL300000086170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086170 none CCC(NN=CC1=CC=C(NC(=O)OC(C)(C)C)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [51, 35, 18, 6, 6, 1, 1, 1, 1, 1, 1, 10, 15, 15, 28, 32, 32, 32, 1, 1, 35, 46, 46, 51, 51, 51, 51, 51, 35, 17, 6, 1, 1, 10, 32, 32, 32, 32, 32, 32, 32, 32, 32] 131 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 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: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086170 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086170 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086170/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086170 Building REAL300000086171 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086171' /scratch/stefan/7769667/working/building/REAL300000086171 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086171 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086171/0 /scratch/stefan/7769667/working/building/REAL300000086171 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/181 `/scratch/stefan/7769667/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(CNC(=O)OC(C)(C)C)NN=C(CC)C(=O)[O-]) `REAL300000086171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086171 none CCOCC(CNC(=O)OC(C)(C)C)NN=C(CC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 1, 1, 2, 3, 5, 5, 9, 10, 10, 10, 1, 3, 6, 6, 11, 6, 9, 9, 3, 3, 3, 3, 3, 2, 2, 1, 2, 2, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 11, 11, 11, 11, 11] 31 rigid atoms, others: [3, 4, 5, 14, 29] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 82 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086171 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086171 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086171/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086171 Building REAL300000086172 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086172' /scratch/stefan/7769667/working/building/REAL300000086172 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086172 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086172/0 /scratch/stefan/7769667/working/building/REAL300000086172 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/182 `/scratch/stefan/7769667/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CCC1=CC=CC=C1)C1=CC=CC=N1)C(=O)[O-]) `REAL300000086172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086172 none CCC(NN=C(CCC1=CC=CC=C1)C1=CC=CC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 136, 85, 32, 32, 6, 3, 1, 1, 1, 1, 1, 1, 1, 32, 76, 76, 76, 76, 76, 136, 170, 170, 177, 177, 177, 177, 177, 136, 85, 6, 6, 3, 3, 1, 1, 1, 1, 1, 76, 76, 76, 76] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39, 40, 41, 42]) total number of confs: 938 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086172 none CCC(NN=C(CCC1=CC=CC=C1)C1=CC=CC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 57, 27, 7, 7, 1, 7, 49, 63, 76, 76, 66, 76, 76, 1, 1, 1, 1, 1, 1, 57, 76, 76, 82, 82, 82, 82, 82, 57, 27, 49, 49, 63, 63, 76, 76, 76, 76, 76, 1, 1, 1, 1] 201 rigid atoms, others: [5, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 727 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086172 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086172 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086172/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086172 Building REAL300000086173 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086173' /scratch/stefan/7769667/working/building/REAL300000086173 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086173 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086173/0 /scratch/stefan/7769667/working/building/REAL300000086173 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/183 `/scratch/stefan/7769667/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN=C(NC(=O)OC(C)(C)C)C=N1)C(=O)[O-]) `REAL300000086173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086173 none CCC(NN=CC1=CN=C(NC(=O)OC(C)(C)C)C=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 22, 5, 5, 1, 1, 1, 1, 1, 1, 9, 16, 16, 36, 44, 44, 44, 1, 1, 46, 62, 62, 64, 64, 64, 64, 64, 46, 22, 5, 1, 9, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 18, 19, 42, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 452 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086173 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086173 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086173/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086173 Building REAL300000086174 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086174' /scratch/stefan/7769667/working/building/REAL300000086174 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086174 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086174/0 /scratch/stefan/7769667/working/building/REAL300000086174 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/184 `/scratch/stefan/7769667/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(C(F)(F)F)C=C1[N+](=O)[O-])C(=O)[O-]) `REAL300000086174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086174 none CCC(NN=CC1=CC=C(C(F)(F)F)C=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.2', 'O.co2', 'O.co2', '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, 5, 15, 15, 15, 1, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 47, 26, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 47, 50, 50, 53, 53, 53, 53, 53, 47, 26, 7, 1, 1, 1] 53 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 226 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086174 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086174 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086174/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086174 Building REAL300000086175 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086175' /scratch/stefan/7769667/working/building/REAL300000086175 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086175 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086175/0 /scratch/stefan/7769667/working/building/REAL300000086175 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/185 `/scratch/stefan/7769667/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(OC)=C(OC)C=C1Cl)C(=O)[O-]) `REAL300000086175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086175 none CCC(NN=CC1=CC(OC)=C(OC)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 8, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [92, 63, 33, 9, 9, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 1, 1, 63, 81, 81, 92, 92, 92, 92, 92, 63, 33, 9, 1, 3, 4, 4, 4, 4, 4, 1] 123 rigid atoms, others: [35, 5, 6, 7, 8, 9, 11, 12, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 10, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 469 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086175 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086175 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086175/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086175 Building REAL300000086176 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086176' /scratch/stefan/7769667/working/building/REAL300000086176 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086176 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086176/0 /scratch/stefan/7769667/working/building/REAL300000086176 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/186 `/scratch/stefan/7769667/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(CNC(=O)OC(C)(C)C)=C1)C(=O)[O-]) `REAL300000086176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086176 none CCC(NN=CC1=CC=CC(CNC(=O)OC(C)(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 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, 7, 7, 7] 0 hydrogens 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, 13, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 32, 58, 58, 69, 69, 68, 69, 1, 13, 13, 13, 21, 21, 21, 21, 21, 13, 12, 6, 1, 1, 1, 7, 7, 32, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 47, 20] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086176 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086176 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086176/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086176 Building REAL300000086177 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086177' /scratch/stefan/7769667/working/building/REAL300000086177 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086177 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086177/0 /scratch/stefan/7769667/working/building/REAL300000086177 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/187 `/scratch/stefan/7769667/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(F)C=CC(C(F)(F)F)=C1Br)C(=O)[O-]) `REAL300000086177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086177 none CCC(NN=CC1=C(F)C=CC(C(F)(F)F)=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 74, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 76, 76, 81, 81, 81, 81, 81, 74, 50, 11, 1, 1] 81 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086177 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086177 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086177/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086177 Building REAL300000086178 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086178' /scratch/stefan/7769667/working/building/REAL300000086178 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086178 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086178/0 /scratch/stefan/7769667/working/building/REAL300000086178 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/188 `/scratch/stefan/7769667/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(OC2=CC=C(Cl)C=C2)C=C1)C(=O)[O-]) `REAL300000086178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086178 none CCC(NN=C(C)C1=CC=C(OC2=CC=C(Cl)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 49, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 1, 49, 61, 61, 64, 64, 64, 64, 64, 49, 26, 6, 6, 6, 1, 1, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 40, 19, 20, 41] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 337 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086178 none CCC(NN=C(C)C1=CC=C(OC2=CC=C(Cl)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 149, 68, 68, 9, 68, 9, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 198, 201, 201, 200, 201, 201, 201, 201, 198, 150, 68, 68, 68, 19, 19, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [36, 37, 38, 39, 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, 33, 34, 35, 40, 41]) total number of confs: 764 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086178 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086178 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086178/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086178 Building REAL300000086179 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086179' /scratch/stefan/7769667/working/building/REAL300000086179 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086179 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086179/0 /scratch/stefan/7769667/working/building/REAL300000086179 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/189 `/scratch/stefan/7769667/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CSC(NC(=O)OC(C)(C)C)=N1)C(=O)[O-]) `REAL300000086179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086179 none CCC(NN=CC1=CSC(NC(=O)OC(C)(C)C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 14, 1, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 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] 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: [45, 33, 16, 6, 6, 1, 1, 1, 1, 1, 1, 6, 9, 9, 18, 19, 19, 19, 1, 33, 42, 42, 45, 45, 45, 45, 45, 33, 16, 6, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20] 110 rigid atoms, others: [5, 6, 7, 8, 9, 10, 18, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086179 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086179 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086179/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086179 Building REAL300000086180 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086180' /scratch/stefan/7769667/working/building/REAL300000086180 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086180 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086180/0 /scratch/stefan/7769667/working/building/REAL300000086180 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/190 `/scratch/stefan/7769667/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(C2=CC=CC=C2)C(Cl)=C1)C(=O)[O-]) `REAL300000086180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086180 none CCC(NN=CC1=CC=C(C2=CC=CC=C2)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 71, 40, 9, 9, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 1, 71, 74, 74, 88, 88, 88, 88, 88, 71, 40, 9, 1, 1, 4, 4, 3, 4, 4, 1] 88 rigid atoms, others: [5, 6, 7, 8, 9, 10, 16, 17, 18, 37, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 366 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086180 none CCC(NN=CC1=CC=C(C2=CC=CC=C2)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 80, 57, 22, 22, 2, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 80, 82, 82, 88, 88, 88, 88, 88, 80, 57, 22, 4, 4, 1, 1, 1, 1, 1, 4] 88 rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086180 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086180 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086180/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086180 Building REAL300000086181 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086181' /scratch/stefan/7769667/working/building/REAL300000086181 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086181 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086181/0 /scratch/stefan/7769667/working/building/REAL300000086181 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/191 `/scratch/stefan/7769667/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=C(C)C=C1Br)C(=O)[O-]) `REAL300000086181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086181 none CCC(NN=CC1=CC(Br)=C(C)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 5, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 41, 41, 50, 50, 50, 50, 50, 40, 26, 9, 1, 2, 2, 2, 1] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 30] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086181 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086181 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086181/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086181 Building REAL300000086182 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086182' /scratch/stefan/7769667/working/building/REAL300000086182 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086182 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086182/0 /scratch/stefan/7769667/working/building/REAL300000086182 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/192 `/scratch/stefan/7769667/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(Br)C(F)=C1F)C(=O)[O-]) `REAL300000086182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086182 none CCC(NN=CC1=CC=C(Br)C(F)=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 17, 1, 15, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 36, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 37, 37, 46, 46, 46, 46, 46, 36, 26, 8, 1, 1] 46 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086182 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086182 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086182/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086182 Building REAL300000086183 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086183' /scratch/stefan/7769667/working/building/REAL300000086183 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086183 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086183/0 /scratch/stefan/7769667/working/building/REAL300000086183 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/193 `/scratch/stefan/7769667/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(C2=CC=C(NC(=O)OC(C)(C)C)C=C2)=N1)C(=O)[O-]) `REAL300000086183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086183 none CCC(NN=CC1=CC=CC(C2=CC=C(NC(=O)OC(C)(C)C)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 14, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 21, 40, 40, 72, 75, 75, 75, 6, 6, 1, 14, 21, 21, 22, 22, 22, 22, 22, 14, 6, 4, 1, 1, 1, 6, 6, 21, 75, 75, 75, 75, 75, 75, 75, 75, 75, 6, 6] 201 rigid atoms, others: [11, 37, 6, 7, 8, 9, 10, 39, 25, 38, 5] 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, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 339 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086183 none CCC(NN=CC1=CC=CC(C2=CC=C(NC(=O)OC(C)(C)C)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 45, 23, 14, 14, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 9, 9, 19, 21, 21, 21, 1, 1, 6, 45, 58, 58, 61, 61, 61, 61, 61, 45, 23, 14, 6, 6, 6, 1, 1, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1] 201 rigid atoms, others: [40, 41, 10, 11, 12, 13, 14, 15, 52, 53, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 386 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086183 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086183 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086183/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086183 Building REAL300000086184 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086184' /scratch/stefan/7769667/working/building/REAL300000086184 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086184 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086184/0 /scratch/stefan/7769667/working/building/REAL300000086184 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/194 `/scratch/stefan/7769667/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=C(C(C)OCOC)C=C1F)C(=O)[O-]) `REAL300000086184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086184 none CCC(NN=CC1=CC(Br)=C(C(C)OCOC)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 17, 1, 5, 5, 12, 5, 12, 5, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 40, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 28, 71, 1, 1, 1, 40, 62, 62, 69, 69, 69, 69, 69, 40, 19, 5, 1, 4, 4, 4, 4, 28, 28, 71, 71, 71, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 41, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 525 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086184 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086184 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086184/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086184 Building REAL300000086185 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086185' /scratch/stefan/7769667/working/building/REAL300000086185 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086185 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086185/0 /scratch/stefan/7769667/working/building/REAL300000086185 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/195 `/scratch/stefan/7769667/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CNN=C1CN1C(=O)C2=CC=CC=C2C1=O)C(=O)[O-]) `REAL300000086185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086185 none CCC(NN=CC1=CNN=C1CN1C(=O)C2=CC=CC=C2C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 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: [82, 56, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 56, 70, 70, 82, 82, 82, 82, 82, 56, 26, 9, 1, 1, 7, 7, 15, 15, 15, 15] 140 rigid atoms, others: [34, 35, 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, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 449 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086185 none CCC(NN=CC1=CNN=C1CN1C(=O)C2=CC=CC=C2C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 34, 27, 17, 17, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 36, 36, 36, 36, 36, 36, 36, 34, 27, 17, 13, 13, 6, 6, 1, 1, 1, 1] 36 rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086185 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086185 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086185/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086185 Building REAL300000086186 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086186' /scratch/stefan/7769667/working/building/REAL300000086186 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086186 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086186/0 /scratch/stefan/7769667/working/building/REAL300000086186 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/196 `/scratch/stefan/7769667/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(F)=C1OC(F)(F)F)C(=O)[O-]) `REAL300000086186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086186 none CCC(NN=CC1=CC=CC(F)=C1OC(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', '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, 15, 1, 12, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 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: [80, 48, 24, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 48, 71, 71, 80, 80, 80, 80, 80, 48, 24, 4, 1, 1, 1] 143 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 489 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086186 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086186 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086186/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086186 Building REAL300000086187 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086187' /scratch/stefan/7769667/working/building/REAL300000086187 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086187 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086187/0 /scratch/stefan/7769667/working/building/REAL300000086187 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/197 `/scratch/stefan/7769667/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(C(=O)N2CCCC2)C=C1)C(=O)[O-]) `REAL300000086187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086187 none CCC(NN=CC1=CC=C(C(=O)N2CCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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, 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: [82, 59, 28, 5, 5, 1, 1, 1, 1, 1, 1, 9, 9, 20, 20, 20, 20, 1, 1, 59, 73, 73, 82, 82, 82, 82, 82, 59, 27, 5, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1] 141 rigid atoms, others: [5, 6, 7, 8, 9, 10, 17, 18, 41, 40, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 429 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086187 none CCC(NN=CC1=CC=C(C(=O)N2CCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 123, 97, 33, 33, 7, 11, 20, 20, 7, 1, 7, 1, 1, 1, 1, 1, 20, 20, 123, 132, 132, 141, 141, 141, 141, 141, 123, 97, 33, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 141 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41]) total number of confs: 571 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086187 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086187 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086187/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086187 Building REAL300000086188 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086188' /scratch/stefan/7769667/working/building/REAL300000086188 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086188 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086188/0 /scratch/stefan/7769667/working/building/REAL300000086188 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/198 `/scratch/stefan/7769667/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(C)C(Br)=C1C)C(=O)[O-]) `REAL300000086188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086188 none CCC(NN=CC1=CC=C(C)C(Br)=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 5, 1, 17, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 47, 33, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 48, 48, 59, 59, 59, 59, 59, 47, 33, 11, 1, 1, 2, 2, 2, 2, 2, 2] 59 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 245 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086188 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086188 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086188/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086188 Building REAL300000086189 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086189' /scratch/stefan/7769667/working/building/REAL300000086189 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086189 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086189/0 /scratch/stefan/7769667/working/building/REAL300000086189 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/199 `/scratch/stefan/7769667/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=NC2=C(C(=O)OC)C=CC=C12)C(=O)[O-]) `REAL300000086189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086189 none CCC(NN=CC1=CC=NC2=C(C(=O)OC)C=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 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: [131, 96, 57, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 1, 1, 1, 1, 96, 115, 115, 131, 131, 131, 131, 131, 96, 57, 12, 1, 1, 13, 13, 13, 1, 1, 1] 201 rigid atoms, others: [32, 36, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 38, 37, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 639 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086189 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086189 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086189/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086189 Building REAL300000086190 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086190' /scratch/stefan/7769667/working/building/REAL300000086190 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086190 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086190/0 /scratch/stefan/7769667/working/building/REAL300000086190 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/200 `/scratch/stefan/7769667/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(Br)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300000086190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086190 none CCC(NN=C(C)C1=CC=C(Br)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [104, 82, 51, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 82, 89, 89, 104, 104, 104, 104, 104, 82, 51, 12, 12, 12, 1, 1, 1] 104 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 12, 13, 16, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 445 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086190 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086190 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086190/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086190 Building REAL300000086191 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086191' /scratch/stefan/7769667/working/building/REAL300000086191 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086191 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086191/0 /scratch/stefan/7769667/working/building/REAL300000086191 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/201 `/scratch/stefan/7769667/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(OCCN2CCOCC2)C=C1)C(=O)[O-]) `REAL300000086191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086191 none CCC(NN=CC1=CC=C(OCCN2CCOCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 12, 5, 5, 1, 1, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 28, 14, 5, 5, 1, 1, 1, 1, 1, 1, 6, 19, 39, 58, 58, 58, 58, 58, 1, 1, 28, 36, 36, 38, 38, 38, 38, 38, 28, 14, 5, 1, 1, 19, 19, 39, 39, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 46, 47, 19, 20] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 372 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086191 none CCC(NN=CC1=CC=C(OCCN2CCOCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 12, 5, 5, 1, 1, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 142, 98, 98, 58, 44, 58, 58, 24, 7, 5, 1, 1, 1, 1, 1, 1, 1, 58, 58, 201, 201, 201, 201, 201, 201, 201, 201, 201, 142, 98, 58, 58, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58] 201 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 44] 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, 35, 36, 37, 46, 47]) total number of confs: 770 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086191 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086191 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086191/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086191 Building REAL300000086192 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086192' /scratch/stefan/7769667/working/building/REAL300000086192 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086192 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086192/0 /scratch/stefan/7769667/working/building/REAL300000086192 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/202 `/scratch/stefan/7769667/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CNC2=CC=CC(NC(=O)OC(C)(C)C)=C12)C(=O)[O-]) `REAL300000086192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086192 none CCC(NN=CC1=CNC2=CC=CC(NC(=O)OC(C)(C)C)=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 3, 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, 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, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 5 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 38, 37] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086192 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086192 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086192/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086192 Building REAL300000086193 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086193' /scratch/stefan/7769667/working/building/REAL300000086193 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086193 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086193/0 /scratch/stefan/7769667/working/building/REAL300000086193 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/203 `/scratch/stefan/7769667/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C=CC1=CC=C(CNN=C(CC)C(=O)[O-])N1C) `REAL300000086193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086193 none CCOC(=O)C=CC1=CC=C(CNN=C(CC)C(=O)[O-])N1C 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.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'H', 'H', '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, 1, 1, 1, 1, 5, 8, 8, 1, 5, 5, 1, 11, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7] 0 hydrogens 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, 16, 16, 10, 16, 10, 1, 1, 1, 1, 1, 1, 5, 17, 34, 34, 78, 34, 44, 44, 1, 1, 26, 26, 26, 26, 26, 10, 10, 1, 1, 5, 5, 17, 78, 78, 78, 78, 78, 2, 2, 2] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 428 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086193 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086193 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086193/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086193 Building REAL300000086194 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086194' /scratch/stefan/7769667/working/building/REAL300000086194 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086194 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086194/0 /scratch/stefan/7769667/working/building/REAL300000086194 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/204 `/scratch/stefan/7769667/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN1C=C(C=NNC(CC)C(=O)[O-])C(C2=CC=CC=C2)=N1) `REAL300000086194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086194 none CCOC(=O)CN1C=C(C=NNC(CC)C(=O)[O-])C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 52, 41, 6, 41, 1, 1, 1, 1, 1, 4, 4, 9, 16, 20, 16, 20, 20, 1, 1, 6, 6, 1, 6, 6, 1, 86, 86, 86, 86, 86, 6, 6, 1, 4, 9, 16, 20, 20, 20, 20, 20, 6, 6, 2, 6, 6] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 18, 19, 25] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086194 none CCOC(=O)CN1C=C(C=NNC(CC)C(=O)[O-])C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 86, 76, 17, 76, 6, 6, 6, 6, 6, 9, 9, 17, 26, 31, 26, 31, 31, 1, 1, 1, 1, 1, 1, 1, 6, 121, 121, 121, 121, 121, 17, 17, 6, 9, 17, 26, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 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, 40, 41]) total number of confs: 546 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086194 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086194 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086194/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086194 Building REAL300000086195 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086195' /scratch/stefan/7769667/working/building/REAL300000086195 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086195 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086195/0 /scratch/stefan/7769667/working/building/REAL300000086195 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/205 `/scratch/stefan/7769667/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(C)N=C1C1=CC(F)=CC=C1F)C(=O)[O-]) `REAL300000086195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086195 none CCC(NN=CC1=CN(C)N=C1C1=CC(F)=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 8, 8, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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] 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, 12, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 12, 12, 12, 15, 15, 15, 15, 15, 12, 11, 7, 1, 2, 2, 2, 7, 6, 7] 25 rigid atoms, others: [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, 32, 33, 34, 35, 36, 37]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086195 none CCC(NN=CC1=CN(C)N=C1C1=CC(F)=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 8, 8, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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] 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, 23, 14, 14, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 23, 14, 7, 7, 7, 7, 1, 1, 1] 25 rigid atoms, others: [35, 36, 37, 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, 32, 33, 34]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086195 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086195 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086195/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086195 Building REAL300000086196 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086196' /scratch/stefan/7769667/working/building/REAL300000086196 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086196 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086196/0 /scratch/stefan/7769667/working/building/REAL300000086196 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/206 `/scratch/stefan/7769667/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=C(C=NNC(CC)C(=O)[O-])N1S(=O)(=O)N(C)C) `REAL300000086196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086196 none CCC1=NC=C(C=NNC(CC)C(=O)[O-])N1S(=O)(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 8, 14, 11, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 7, 7, 37, 69, 105, 69, 94, 94, 1, 1, 10, 10, 10, 13, 13, 5, 5, 5, 4, 4, 1, 7, 37, 69, 105, 105, 105, 105, 105, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 15, 16, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 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: 591 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086196 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086196 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086196/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086196 Building REAL300000086197 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086197' /scratch/stefan/7769667/working/building/REAL300000086197 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086197 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086197/0 /scratch/stefan/7769667/working/building/REAL300000086197 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/207 `/scratch/stefan/7769667/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(C(=O)OC)C(Br)=C1)C(=O)[O-]) `REAL300000086197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086197 none CCC(NN=CC1=CC=C(C(=O)OC)C(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'Br', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 101, 51, 10, 10, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1, 1, 101, 131, 131, 152, 152, 152, 152, 152, 101, 51, 10, 1, 1, 7, 7, 7, 1] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32]) total number of confs: 784 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086197 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086197 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086197/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086197 Building REAL300000086198 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086198' /scratch/stefan/7769667/working/building/REAL300000086198 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086198 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086198/0 /scratch/stefan/7769667/working/building/REAL300000086198 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/208 `/scratch/stefan/7769667/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Cl)=CC(Br)=C1[O-])C(=O)[O-]) `REAL300000086198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086198 none CCC(NN=CC1=CC(Cl)=CC(Br)=C1[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 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, 18, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 19, 19, 25, 25, 25, 25, 25, 18, 13, 4, 1, 1] 25 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086198 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086198/1 /scratch/stefan/7769667/working/building/REAL300000086198 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/209 `/scratch/stefan/7769667/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Cl)=CC(Br)=C1O)C(=O)[O-]) `REAL300000086198.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086198 none CCC(NN=CC1=CC(Cl)=CC(Br)=C1O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 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, 30, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 40, 40, 40, 40, 40, 30, 22, 7, 1, 1, 2] 80 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28]) total number of confs: 152 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086198 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086198 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086198/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086198/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086198 Building REAL300000086199 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086199' /scratch/stefan/7769667/working/building/REAL300000086199 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086199 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086199/0 /scratch/stefan/7769667/working/building/REAL300000086199 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/210 `/scratch/stefan/7769667/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=CC(F)=C1[O-])C(=O)[O-]) `REAL300000086199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086199 none CCC(NN=CC1=CC(Br)=CC(F)=C1[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 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, 17, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 18, 18, 25, 25, 25, 25, 25, 17, 12, 4, 1, 1] 25 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086199 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086199/1 /scratch/stefan/7769667/working/building/REAL300000086199 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/211 `/scratch/stefan/7769667/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=CC(F)=C1O)C(=O)[O-]) `REAL300000086199.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086199 none CCC(NN=CC1=CC(Br)=CC(F)=C1O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [36, 27, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 36, 36, 36, 36, 36, 27, 19, 5, 1, 1, 2] 72 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28]) total number of confs: 143 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086199 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086199 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086199/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086199/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086199 Building REAL300000086200 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086200' /scratch/stefan/7769667/working/building/REAL300000086200 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086200 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086200/0 /scratch/stefan/7769667/working/building/REAL300000086200 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/212 `/scratch/stefan/7769667/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(Br)C=C1C)C(=O)[O-]) `REAL300000086200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086200 none CCC(NN=C(C)C1=CC=C(Br)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 50, 33, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 50, 51, 51, 63, 63, 63, 63, 63, 50, 33, 10, 10, 10, 1, 1, 1, 2, 2, 2] 63 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 246 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086200 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086200 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086200/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086200 Building REAL300000086201 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086201' /scratch/stefan/7769667/working/building/REAL300000086201 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086201 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086201/0 /scratch/stefan/7769667/working/building/REAL300000086201 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/213 `/scratch/stefan/7769667/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=CC=C1OC1=CC=CC(Cl)=C1)C(=O)[O-]) `REAL300000086201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086201 none CCC(NN=C(C)C1=CC=CC=C1OC1=CC=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [20, 16, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 6, 31, 31, 31, 31, 31, 31, 16, 18, 18, 20, 20, 20, 20, 20, 16, 11, 5, 5, 5, 1, 1, 1, 1, 31, 31, 31, 31] 111 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086201 none CCC(NN=C(C)C1=CC=CC=C1OC1=CC=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 92, 71, 45, 45, 31, 45, 31, 31, 31, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 92, 111, 111, 111, 111, 111, 111, 111, 92, 71, 45, 45, 45, 31, 31, 31, 31, 1, 1, 1, 1] 111 rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 466 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086201 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086201 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086201/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086201 Building REAL300000086202 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086202' /scratch/stefan/7769667/working/building/REAL300000086202 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086202 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086202/0 /scratch/stefan/7769667/working/building/REAL300000086202 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/214 `/scratch/stefan/7769667/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC(F)=CC=C1OC1=CC=CC(F)=C1)C(=O)[O-]) `REAL300000086202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086202 none CCC(NN=C(C)C1=CC(F)=CC=C1OC1=CC=CC(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [44, 23, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 30, 30, 30, 30, 30, 30, 23, 29, 29, 44, 44, 44, 44, 44, 23, 15, 7, 7, 7, 1, 1, 1, 30, 30, 30, 30] 138 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 245 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086202 none CCC(NN=C(C)C1=CC(F)=CC=C1OC1=CC=CC(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [138, 122, 88, 48, 48, 30, 48, 30, 30, 30, 30, 30, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 122, 138, 138, 138, 138, 138, 138, 138, 122, 88, 48, 48, 48, 30, 30, 30, 1, 1, 1, 1] 138 rigid atoms, others: [38, 39, 40, 41, 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, 35, 36, 37]) total number of confs: 550 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086202 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086202 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086202/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086202 Building REAL300000086203 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086203' /scratch/stefan/7769667/working/building/REAL300000086203 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086203 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086203/0 /scratch/stefan/7769667/working/building/REAL300000086203 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/215 `/scratch/stefan/7769667/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(OC2=CC=CC=C2Cl)C=C1Cl)C(=O)[O-]) `REAL300000086203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086203 none CCC(NN=C(C)C1=CC=C(OC2=CC=CC=C2Cl)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', '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, 12, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 32, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 9, 23, 23, 9, 23, 23, 23, 1, 1, 1, 32, 35, 35, 37, 37, 37, 37, 37, 32, 22, 7, 7, 7, 1, 1, 23, 23, 15, 23, 1] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 21, 41] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086203 none CCC(NN=C(C)C1=CC=C(OC2=CC=CC=C2Cl)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', '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, 12, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 147, 92, 92, 23, 92, 23, 23, 23, 8, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 92, 92, 92, 23, 23, 1, 1, 1, 1, 23] 201 rigid atoms, others: [37, 38, 39, 40, 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, 33, 34, 35, 36, 41]) total number of confs: 713 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086203 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086203 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086203/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086203 Building REAL300000086204 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086204' /scratch/stefan/7769667/working/building/REAL300000086204 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086204 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086204/0 /scratch/stefan/7769667/working/building/REAL300000086204 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/216 `/scratch/stefan/7769667/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(F)=CC=C1OC1=CN=CC(Cl)=C1)C(=O)[O-]) `REAL300000086204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086204 none CCC(NN=CC1=CC(F)=CC=C1OC1=CN=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 8, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [17, 12, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 31, 31, 31, 31, 31, 31, 12, 14, 14, 17, 17, 17, 17, 17, 12, 7, 4, 1, 1, 1, 31, 31, 31] 136 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 115 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086204 none CCC(NN=CC1=CC(F)=CC=C1OC1=CN=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 8, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 124, 69, 43, 43, 31, 31, 31, 31, 31, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 124, 136, 136, 136, 136, 136, 136, 136, 124, 69, 43, 31, 31, 31, 1, 1, 1] 136 rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 567 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086204 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086204 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086204/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086204 Building REAL300000086205 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086205' /scratch/stefan/7769667/working/building/REAL300000086205 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086205 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086205/0 /scratch/stefan/7769667/working/building/REAL300000086205 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/217 `/scratch/stefan/7769667/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC([N+](=O)[O-])=CC=C1SC)C(=O)[O-]) `REAL300000086205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086205 none CCC(NN=C(C)C1=CC([N+](=O)[O-])=CC=C1SC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [35, 27, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 30, 30, 35, 35, 35, 35, 35, 27, 17, 5, 5, 5, 1, 1, 1, 7, 7, 7] 47 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086205 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086205 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086205/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086205 Building REAL300000086206 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086206' /scratch/stefan/7769667/working/building/REAL300000086206 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086206 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086206/0 /scratch/stefan/7769667/working/building/REAL300000086206 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/218 `/scratch/stefan/7769667/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(COC(C)C)CC1=CC=C(F)C=C1)C(=O)[O-]) `REAL300000086206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086206 none CCC(NN=C(COC(C)C)CC1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 75, 42, 12, 12, 3, 12, 36, 69, 92, 92, 1, 1, 1, 1, 1, 1, 1, 1, 75, 95, 95, 101, 101, 101, 101, 101, 75, 42, 36, 36, 92, 92, 92, 92, 92, 92, 92, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 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, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 807 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086206 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086206 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086206/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086206 Building REAL300000086207 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086207' /scratch/stefan/7769667/working/building/REAL300000086207 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086207 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086207/0 /scratch/stefan/7769667/working/building/REAL300000086207 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/219 `/scratch/stefan/7769667/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C(=O)NC2=CC=C(OC)C(OC)=C21)C(=O)[O-]) `REAL300000086207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086207 none CCC(NN=C1C(=O)NC2=CC=C(OC)C(OC)=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 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: [27, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 6, 1, 17, 24, 24, 27, 27, 27, 27, 27, 17, 5, 1, 1, 1, 4, 4, 4, 7, 7, 7] 42 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 18, 29, 30, 31] set([0, 1, 2, 35, 36, 33, 32, 34, 14, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086207 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086207 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086207/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086207 Building REAL300000086208 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086208' /scratch/stefan/7769667/working/building/REAL300000086208 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086208 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086208/0 /scratch/stefan/7769667/working/building/REAL300000086208 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/220 `/scratch/stefan/7769667/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(CC)N=C1C1=CC=CC=C1)C(=O)[O-]) `REAL300000086208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086208 none CCC(NN=CC1=CN(CC)N=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 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: [55, 35, 14, 7, 7, 1, 1, 1, 1, 1, 9, 1, 1, 1, 6, 6, 1, 6, 6, 35, 46, 46, 55, 55, 55, 55, 55, 35, 14, 7, 1, 9, 9, 9, 9, 9, 6, 6, 1, 6, 6] 127 rigid atoms, others: [5, 6, 7, 8, 9, 11, 12, 13, 30] set([0, 1, 2, 3, 4, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086208 none CCC(NN=CC1=CN(CC)N=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 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: [82, 56, 28, 15, 15, 6, 6, 6, 6, 6, 32, 6, 1, 1, 1, 1, 1, 1, 1, 56, 65, 65, 82, 82, 82, 82, 82, 56, 28, 15, 6, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1] 127 rigid atoms, others: [36, 37, 38, 39, 40, 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, 35]) total number of confs: 479 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086208 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086208 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086208/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086208 Building REAL300000086209 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086209' /scratch/stefan/7769667/working/building/REAL300000086209 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086209 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086209/0 /scratch/stefan/7769667/working/building/REAL300000086209 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/221 `/scratch/stefan/7769667/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(OC2=CC=C(F)C(C)=C2)C=C1Cl)C(=O)[O-]) `REAL300000086209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086209 none CCC(NN=CC1=CC=C(OC2=CC=C(F)C(C)=C2)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', '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, 12, 1, 1, 1, 1, 15, 1, 5, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 9, 4, 4, 1, 1, 1, 1, 1, 1, 9, 36, 37, 16, 37, 37, 37, 37, 1, 1, 1, 18, 24, 24, 26, 26, 26, 26, 26, 18, 9, 4, 1, 1, 37, 36, 37, 37, 37, 37, 1] 201 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 19, 20, 21, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086209 none CCC(NN=CC1=CC=C(OC2=CC=C(F)C(C)=C2)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', '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, 12, 1, 1, 1, 1, 15, 1, 5, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 137, 104, 104, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 199, 201, 201, 201, 201, 201, 201, 201, 199, 137, 104, 37, 37, 1, 1, 2, 2, 2, 1, 37] 201 rigid atoms, others: [35, 36, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 41]) total number of confs: 762 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086209 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086209 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086209/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086209 Building REAL300000086210 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086210' /scratch/stefan/7769667/working/building/REAL300000086210 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086210 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086210/0 /scratch/stefan/7769667/working/building/REAL300000086210 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/222 `/scratch/stefan/7769667/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC=C1OC1=CC=C(C=NNC(CC)C(=O)[O-])C(Cl)=C1) `REAL300000086210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086210 none CCC1=CC=CC=C1OC1=CC=C(C=NNC(CC)C(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 55, 55, 109, 124, 140, 124, 126, 126, 19, 19, 19, 6, 6, 6, 6, 6, 1, 1, 1, 1, 19, 19, 55, 109, 124, 140, 140, 140, 140, 140, 19] 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, 44]) total number of confs: 517 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086210 none CCC1=CC=CC=C1OC1=CC=C(C=NNC(CC)C(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 19, 19, 19, 15, 19, 19, 9, 1, 1, 1, 1, 1, 1, 4, 4, 14, 19, 26, 19, 22, 22, 1, 1, 1, 39, 39, 39, 39, 39, 19, 15, 19, 19, 1, 1, 4, 14, 19, 26, 26, 26, 26, 26, 1] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 44, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 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]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086210 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086210 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086210/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086210 Building REAL300000086211 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086211' /scratch/stefan/7769667/working/building/REAL300000086211 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086211 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086211/0 /scratch/stefan/7769667/working/building/REAL300000086211 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/223 `/scratch/stefan/7769667/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1OC1=CC=C(F)C(Cl)=C1)C(=O)[O-]) `REAL300000086211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086211 none CCC(NN=CC1=CC=CC=C1OC1=CC=C(F)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'F', 'C.ar', 'Cl', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [18, 12, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 31, 31, 31, 31, 31, 31, 31, 12, 14, 14, 18, 18, 18, 18, 18, 12, 9, 4, 1, 1, 1, 1, 31, 31, 31] 115 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12] 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, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086211 none CCC(NN=CC1=CC=CC=C1OC1=CC=C(F)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'F', 'C.ar', 'Cl', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [115, 103, 66, 42, 42, 31, 31, 31, 31, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 115, 115, 115, 115, 115, 115, 115, 103, 66, 42, 31, 31, 31, 31, 1, 1, 1] 115 rigid atoms, others: [36, 37, 38, 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: 463 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086211 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086211 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086211/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086211 Building REAL300000086212 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086212' /scratch/stefan/7769667/working/building/REAL300000086212 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086212 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086212/0 /scratch/stefan/7769667/working/building/REAL300000086212 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/224 `/scratch/stefan/7769667/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1C)C(=O)[O-]) `REAL300000086212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086212 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [19, 13, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 12, 13, 15, 15, 15, 13, 17, 17, 19, 19, 19, 19, 19, 13, 7, 4, 1, 1, 1, 15, 15, 15, 15, 15, 15] 57 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086212 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 50, 30, 20, 20, 15, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 57, 57, 57, 57, 57, 57, 57, 50, 30, 20, 15, 15, 15, 1, 1, 1, 2, 2, 2] 57 rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086212 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086212 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086212/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086212 Building REAL300000086213 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086213' /scratch/stefan/7769667/working/building/REAL300000086213 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086213 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086213/0 /scratch/stefan/7769667/working/building/REAL300000086213 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/225 `/scratch/stefan/7769667/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(Cl)C=C1OC1=CC=C(F)C(C)=C1)C(=O)[O-]) `REAL300000086213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086213 none CCC(NN=CC1=CC=C(Cl)C=C1OC1=CC=C(F)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 16, 1, 1, 12, 1, 1, 1, 1, 15, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [28, 15, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 31, 31, 10, 31, 31, 31, 31, 15, 21, 21, 28, 28, 28, 28, 28, 15, 9, 4, 1, 1, 1, 31, 31, 31, 31, 31, 31] 141 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 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]) total number of confs: 242 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086213 none CCC(NN=CC1=CC=C(Cl)C=C1OC1=CC=C(F)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 16, 1, 1, 12, 1, 1, 1, 1, 15, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 129, 68, 45, 45, 31, 31, 31, 9, 31, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 129, 141, 141, 141, 141, 141, 141, 141, 129, 68, 45, 31, 31, 31, 1, 1, 2, 2, 2, 1] 141 rigid atoms, others: [36, 37, 41, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 656 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086213 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086213 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086213/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086213 Building REAL300000086214 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086214' /scratch/stefan/7769667/working/building/REAL300000086214 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086214 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086214/0 /scratch/stefan/7769667/working/building/REAL300000086214 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/226 `/scratch/stefan/7769667/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C(Cl)=C1)C(=O)[O-]) `REAL300000086214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086214 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [17, 13, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 30, 30, 30, 30, 30, 30, 30, 13, 17, 17, 17, 17, 17, 17, 17, 13, 8, 4, 1, 1, 1, 30, 30, 30] 133 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 120 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086214 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 123, 68, 45, 45, 30, 30, 30, 30, 30, 30, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 123, 133, 133, 133, 133, 133, 133, 133, 123, 68, 45, 30, 29, 30, 1, 1, 1] 133 rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 557 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086214 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086214 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086214/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086214 Building REAL300000086215 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086215' /scratch/stefan/7769667/working/building/REAL300000086215 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086215 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086215/0 /scratch/stefan/7769667/working/building/REAL300000086215 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/227 `/scratch/stefan/7769667/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C(F)=C1)C(=O)[O-]) `REAL300000086215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086215 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', '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, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [30, 15, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 29, 29, 29, 29, 29, 29, 29, 15, 22, 22, 30, 30, 30, 30, 30, 15, 9, 4, 1, 1, 1, 29, 29, 29] 135 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086215 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', '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, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [135, 123, 74, 44, 44, 29, 29, 29, 29, 29, 29, 28, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 123, 135, 135, 135, 135, 135, 135, 135, 123, 74, 44, 29, 28, 29, 1, 1, 1] 135 rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 548 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086215 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086215 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086215/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086215 Building REAL300000086216 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086216' /scratch/stefan/7769667/working/building/REAL300000086216 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086216 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086216/0 /scratch/stefan/7769667/working/building/REAL300000086216 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/228 `/scratch/stefan/7769667/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1OC1=CC(Cl)=CC=C1C)C(=O)[O-]) `REAL300000086216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086216 none CCC(NN=CC1=CC=CC=C1OC1=CC(Cl)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [18, 11, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 13, 17, 17, 17, 11, 16, 16, 18, 18, 18, 18, 18, 11, 8, 4, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17] 54 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12] 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, 36, 37, 38, 39, 40, 41]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086216 none CCC(NN=CC1=CC=CC=C1OC1=CC(Cl)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 50, 31, 21, 21, 17, 17, 17, 17, 17, 17, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 54, 54, 54, 54, 54, 54, 54, 50, 31, 21, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2] 54 rigid atoms, others: [36, 37, 38, 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, 39, 40, 41]) total number of confs: 211 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086216 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086216 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086216/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086216 Building REAL300000086217 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086217' /scratch/stefan/7769667/working/building/REAL300000086217 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086217 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086217/0 /scratch/stefan/7769667/working/building/REAL300000086217 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/229 `/scratch/stefan/7769667/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(F)=CC=C1OC1=CC=CC(Cl)=C1)C(=O)[O-]) `REAL300000086217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086217 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [20, 13, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 31, 31, 31, 31, 31, 31, 13, 16, 16, 20, 20, 20, 20, 20, 13, 8, 4, 1, 1, 1, 31, 31, 31, 31] 132 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 135 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086217 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [132, 119, 65, 41, 41, 31, 31, 31, 30, 30, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 119, 132, 132, 132, 132, 132, 132, 132, 119, 65, 41, 31, 31, 31, 1, 1, 1, 1] 132 rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 569 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086217 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086217 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086217/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086217 Building REAL300000086218 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086218' /scratch/stefan/7769667/working/building/REAL300000086218 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086218 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086218/0 /scratch/stefan/7769667/working/building/REAL300000086218 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/230 `/scratch/stefan/7769667/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC=C1OC1=CC=C(Cl)C=C1C=NNC(CC)C(=O)[O-]) `REAL300000086218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086218 none CCC1=CC=CC=C1OC1=CC=C(Cl)C=C1C=NNC(CC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 11, 13, 13, 13, 13, 37, 37, 91, 137, 148, 137, 145, 145, 5, 5, 5, 5, 5, 1, 1, 1, 1, 13, 13, 13, 37, 91, 137, 148, 148, 148, 148, 148] 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, 44]) total number of confs: 609 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086218 none CCC1=CC=CC=C1OC1=CC=C(Cl)C=C1C=NNC(CC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 13, 13, 13, 9, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 26, 43, 56, 43, 51, 51, 24, 24, 24, 24, 24, 13, 11, 13, 13, 1, 1, 1, 11, 26, 43, 56, 56, 56, 56, 56] 201 rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 346 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086218 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086218 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086218/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086218 Building REAL300000086219 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086219' /scratch/stefan/7769667/working/building/REAL300000086219 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086219 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086219/0 /scratch/stefan/7769667/working/building/REAL300000086219 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/231 `/scratch/stefan/7769667/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(Cl)C=C1OC1=CC=C(Cl)C(F)=C1)C(=O)[O-]) `REAL300000086219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086219 none CCC(NN=CC1=CC=C(Cl)C=C1OC1=CC=C(Cl)C(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 16, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [31, 15, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 29, 29, 29, 29, 29, 29, 29, 15, 22, 22, 31, 31, 31, 31, 31, 15, 9, 4, 1, 1, 1, 29, 29, 29] 138 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086219 none CCC(NN=CC1=CC=C(Cl)C=C1OC1=CC=C(Cl)C(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 16, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [138, 127, 72, 42, 42, 29, 29, 29, 11, 29, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 127, 138, 138, 138, 138, 138, 138, 138, 127, 72, 42, 29, 29, 29, 1, 1, 1] 138 rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 609 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086219 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086219 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086219/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086219 Building REAL300000086220 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086220' /scratch/stefan/7769667/working/building/REAL300000086220 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086220 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086220/0 /scratch/stefan/7769667/working/building/REAL300000086220 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/232 `/scratch/stefan/7769667/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=C(C)S1)C(=O)[O-]) `REAL300000086220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086220 none CCC(NN=CC1=CC(Br)=C(C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 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: [67, 50, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 50, 53, 53, 67, 67, 67, 67, 67, 50, 31, 6, 1, 2, 2, 2] 68 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 24] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27]) total number of confs: 294 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086220 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086220 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086220/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086220 Building REAL300000086221 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086221' /scratch/stefan/7769667/working/building/REAL300000086221 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086221 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086221/0 /scratch/stefan/7769667/working/building/REAL300000086221 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/233 `/scratch/stefan/7769667/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCCCC2=CC(OC)=C(OC)C=C21)C(=O)[O-]) `REAL300000086221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086221 none CCC(NN=C1CCCCC2=CC(OC)=C(OC)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [30, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 1, 16, 24, 24, 30, 30, 30, 30, 30, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 3, 3, 3, 1] 49 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 18, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45] set([0, 1, 2, 39, 40, 41, 42, 43, 44, 14, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086221 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086221 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086221/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086221 Building REAL300000086222 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086222' /scratch/stefan/7769667/working/building/REAL300000086222 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086222 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086222/0 /scratch/stefan/7769667/working/building/REAL300000086222 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/234 `/scratch/stefan/7769667/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(C2=CC=C(Cl)C=C2)=C1)C(=O)[O-]) `REAL300000086222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086222 none CCC(NN=CC1=CC=CC(C2=CC=C(Cl)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 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: [111, 79, 45, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 79, 91, 91, 111, 111, 111, 111, 111, 79, 45, 11, 1, 1, 1, 3, 3, 3, 3, 1] 130 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 18, 37, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 525 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086222 none CCC(NN=CC1=CC=CC(C2=CC=C(Cl)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [130, 117, 76, 22, 22, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 117, 121, 121, 130, 130, 130, 130, 130, 117, 76, 22, 3, 3, 3, 1, 1, 1, 1, 3] 130 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 494 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086222 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086222 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086222/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086222 Building REAL300000086223 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086223' /scratch/stefan/7769667/working/building/REAL300000086223 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086223 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086223/0 /scratch/stefan/7769667/working/building/REAL300000086223 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/235 `/scratch/stefan/7769667/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(F)=C1I)C(=O)[O-]) `REAL300000086223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086223 none CCC(NN=CC1=CC=CC(F)=C1I)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'I', 'C.2', 'O.co2', 'O.co2', '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, 15, 1, 18, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [53, 37, 27, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 42, 42, 53, 53, 53, 53, 53, 37, 27, 10, 1, 1, 1] 55 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086223 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086223 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086223/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086223 Building REAL300000086224 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086224' /scratch/stefan/7769667/working/building/REAL300000086224 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086224 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086224/0 /scratch/stefan/7769667/working/building/REAL300000086224 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/236 `/scratch/stefan/7769667/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(OC)C(COC2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300000086224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086224 none CCC(NN=CC1=CC=C(OC)C(COC2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 43, 16, 7, 7, 1, 1, 1, 1, 1, 1, 3, 1, 1, 7, 17, 18, 18, 17, 18, 18, 1, 43, 58, 58, 69, 69, 69, 69, 69, 43, 16, 7, 1, 1, 4, 4, 4, 7, 7, 18, 18, 17, 18, 18, 1] 201 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 12, 13, 45, 21] set([0, 1, 2, 3, 4, 11, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 427 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086224 none CCC(NN=CC1=CC=C(OC)C(COC2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [185, 135, 89, 49, 49, 18, 18, 18, 18, 18, 18, 30, 6, 2, 1, 1, 1, 1, 1, 1, 1, 18, 135, 168, 168, 185, 185, 185, 185, 185, 135, 89, 49, 18, 18, 30, 30, 30, 6, 6, 1, 1, 1, 1, 1, 18] 201 rigid atoms, others: [40, 41, 42, 43, 44, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45]) total number of confs: 946 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086224 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086224 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086224/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086224 Building REAL300000086225 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086225' /scratch/stefan/7769667/working/building/REAL300000086225 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086225 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086225/0 /scratch/stefan/7769667/working/building/REAL300000086225 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/237 `/scratch/stefan/7769667/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(OC)C(CN2C=CC=N2)=C1)C(=O)[O-]) `REAL300000086225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086225 none CCC(NN=CC1=CC=C(OC)C(CN2C=CC=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 12, 5, 1, 5, 8, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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] 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: [20, 12, 7, 4, 4, 1, 1, 1, 1, 1, 1, 4, 1, 1, 5, 21, 21, 21, 21, 1, 12, 13, 13, 20, 20, 20, 20, 20, 12, 7, 4, 1, 1, 4, 4, 4, 5, 5, 21, 21, 21, 1] 82 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 12, 13, 19, 41, 31] set([0, 1, 2, 3, 4, 11, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086225 none CCC(NN=CC1=CC=C(OC)C(CN2C=CC=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 12, 5, 1, 5, 8, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 67, 46, 38, 38, 21, 21, 21, 21, 21, 21, 25, 9, 1, 1, 1, 1, 1, 1, 21, 67, 71, 71, 82, 82, 82, 82, 82, 67, 46, 38, 21, 21, 25, 25, 25, 9, 9, 1, 1, 1, 21] 82 rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41]) total number of confs: 351 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086225 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086225 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086225/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086225 Building REAL300000086226 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086226' /scratch/stefan/7769667/working/building/REAL300000086226 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086226 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086226/0 /scratch/stefan/7769667/working/building/REAL300000086226 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/238 `/scratch/stefan/7769667/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C)C=CC(Br)=C1F)C(=O)[O-]) `REAL300000086226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086226 none CCC(NN=CC1=C(C)C=CC(Br)=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 5, 1, 1, 1, 17, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 69, 40, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 76, 76, 97, 97, 97, 97, 97, 69, 40, 10, 2, 2, 2, 1, 1] 97 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 441 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086226 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086226 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086226/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086226 Building REAL300000086227 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086227' /scratch/stefan/7769667/working/building/REAL300000086227 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086227 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086227/0 /scratch/stefan/7769667/working/building/REAL300000086227 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/239 `/scratch/stefan/7769667/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(OC2=CC=C(F)C=C2C=NNC(CC)C(=O)[O-])=CC=C1Cl) `REAL300000086227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086227 none CCC1=CC(OC2=CC=C(F)C=C2C=NNC(CC)C(=O)[O-])=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', '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, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 29, 29, 28, 28, 29, 29, 29, 48, 48, 73, 105, 106, 105, 106, 106, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 29, 29, 29, 48, 73, 105, 106, 106, 106, 106, 106, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 43, 44, 22, 23, 24, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086227 none CCC1=CC(OC2=CC=C(F)C=C2C=NNC(CC)C(=O)[O-])=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', '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, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7] 0 hydrogens 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, 29, 29, 29, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 18, 21, 18, 20, 20, 29, 29, 8, 16, 57, 57, 57, 57, 57, 29, 1, 1, 1, 5, 10, 18, 21, 21, 21, 21, 21, 29, 29] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 346 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086227 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086227 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086227/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086227 Building REAL300000086228 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086228' /scratch/stefan/7769667/working/building/REAL300000086228 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086228 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086228/0 /scratch/stefan/7769667/working/building/REAL300000086228 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/240 `/scratch/stefan/7769667/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1OC1=CC=C(Cl)C(Cl)=C1)C(=O)[O-]) `REAL300000086228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086228 none CCC(NN=CC1=CC=CC=C1OC1=CC=C(Cl)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'Cl', 'C.ar', 'Cl', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [18, 12, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 31, 31, 31, 31, 31, 31, 31, 12, 14, 14, 18, 18, 18, 18, 18, 12, 9, 4, 1, 1, 1, 1, 31, 31, 31] 115 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12] 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, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086228 none CCC(NN=CC1=CC=CC=C1OC1=CC=C(Cl)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'Cl', 'C.ar', 'Cl', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [115, 103, 69, 42, 42, 31, 31, 31, 31, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 115, 115, 115, 115, 115, 115, 115, 103, 69, 42, 31, 31, 31, 31, 1, 1, 1] 115 rigid atoms, others: [36, 37, 38, 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: 464 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086228 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086228 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086228/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086228 Building REAL300000086229 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086229' /scratch/stefan/7769667/working/building/REAL300000086229 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086229 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086229/0 /scratch/stefan/7769667/working/building/REAL300000086229 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/241 `/scratch/stefan/7769667/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(Cl)C=C1OC1=CC=C(C)C=C1C)C(=O)[O-]) `REAL300000086229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086229 none CCC(NN=CC1=CC=C(Cl)C=C1OC1=CC=C(C)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [23, 13, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 8, 8, 15, 15, 15, 13, 17, 17, 23, 23, 23, 23, 23, 13, 7, 4, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15] 57 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 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, 43, 44]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086229 none CCC(NN=CC1=CC=C(Cl)C=C1OC1=CC=C(C)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 50, 26, 20, 20, 15, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 57, 57, 57, 57, 57, 57, 57, 50, 26, 20, 15, 15, 15, 1, 1, 2, 2, 2, 1, 2, 2, 2] 57 rigid atoms, others: [36, 37, 41, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 42, 43, 44]) total number of confs: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086229 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086229 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086229/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086229 Building REAL300000086230 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086230' /scratch/stefan/7769667/working/building/REAL300000086230 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086230 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086230/0 /scratch/stefan/7769667/working/building/REAL300000086230 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/242 `/scratch/stefan/7769667/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC[C@@H]2C[N@H+](CC3=CC=CC=C3)C[C@H]12)C(=O)[O-]) `REAL300000086230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086230 none CCC(NN=C1CC[C@@H]2C[N@H+](CC3=CC=CC=C3)C[C@H]12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 1, 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, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [24, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 10, 1, 1, 1, 15, 19, 19, 24, 24, 24, 24, 24, 15, 6, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 1, 1] 41 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 33, 34, 35, 36, 37, 38, 46, 47] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086230 none CCC(NN=C1CC[C@@H]2C[N@H+](CC3=CC=CC=C3)C[C@H]12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 1, 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, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 40, 26, 10, 10, 10, 10, 10, 10, 10, 10, 4, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 40, 41, 41, 41, 41, 41, 41, 41, 40, 26, 10, 10, 10, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 10, 10] 41 rigid atoms, others: [45, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) total number of confs: 158 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086230 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086230/1 /scratch/stefan/7769667/working/building/REAL300000086230 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/243 `/scratch/stefan/7769667/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC[C@@H]2C[N@@H+](CC3=CC=CC=C3)C[C@H]12)C(=O)[O-]) `REAL300000086230.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086230 none CCC(NN=C1CC[C@@H]2C[N@@H+](CC3=CC=CC=C3)C[C@H]12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 1, 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, 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: [14, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 1, 10, 13, 13, 14, 14, 14, 14, 14, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 1, 1] 33 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 33, 34, 35, 36, 37, 38, 46, 47] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086230 none CCC(NN=C1CC[C@@H]2C[N@@H+](CC3=CC=CC=C3)C[C@H]12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 1, 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, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 25, 15, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 33, 33, 33, 33, 33, 33, 33, 25, 15, 7, 7, 7, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 7, 7] 33 rigid atoms, others: [45, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) total number of confs: 172 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086230 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086230 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086230/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086230/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086230 Building REAL300000086231 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086231' /scratch/stefan/7769667/working/building/REAL300000086231 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086231 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086231/0 /scratch/stefan/7769667/working/building/REAL300000086231 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/244 `/scratch/stefan/7769667/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(CC2=CC=C(OC)C=C2)N=N1)C(=O)[O-]) `REAL300000086231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086231 none CCC(NN=CC1=CN(CC2=CC=C(OC)C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 32, 15, 4, 4, 1, 1, 1, 1, 1, 9, 19, 19, 13, 13, 35, 19, 19, 1, 1, 32, 49, 49, 54, 54, 54, 54, 54, 32, 15, 4, 1, 9, 9, 19, 19, 35, 35, 35, 19, 19] 201 rigid atoms, others: [5, 6, 7, 8, 9, 18, 19, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 404 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086231 none CCC(NN=CC1=CN(CC2=CC=C(OC)C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 159, 104, 37, 37, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 2, 1, 1, 19, 19, 159, 190, 190, 199, 199, 199, 199, 199, 159, 104, 37, 19, 5, 5, 1, 1, 3, 3, 3, 1, 1] 201 rigid atoms, others: [34, 35, 39, 40, 9, 10, 11, 12, 13, 14, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 921 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086231 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086231 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086231/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086231 Building REAL300000086232 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086232' /scratch/stefan/7769667/working/building/REAL300000086232 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086232 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086232/0 /scratch/stefan/7769667/working/building/REAL300000086232 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/245 `/scratch/stefan/7769667/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(OCC2=CC=CC(OC)=C2)C=C1)C(=O)[O-]) `REAL300000086232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086232 none CCC(NN=CC1=CC=C(OCC2=CC=CC(OC)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 27, 13, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 16, 16, 16, 16, 16, 31, 16, 1, 1, 27, 37, 37, 38, 38, 38, 38, 38, 27, 13, 3, 1, 1, 2, 2, 16, 16, 16, 32, 32, 32, 16, 1, 1] 201 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 44, 45, 20, 21] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086232 none CCC(NN=CC1=CC=C(OCC2=CC=CC(OC)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 105, 46, 46, 16, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 1, 16, 16, 163, 194, 194, 201, 201, 201, 201, 201, 163, 105, 46, 16, 16, 8, 8, 1, 1, 1, 3, 3, 3, 1, 16, 16] 201 rigid atoms, others: [43, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 44, 45]) total number of confs: 957 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086232 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086232 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086232/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086232 Building REAL300000086233 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086233' /scratch/stefan/7769667/working/building/REAL300000086233 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086233 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086233/0 /scratch/stefan/7769667/working/building/REAL300000086233 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/246 `/scratch/stefan/7769667/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(COC2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300000086233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086233 none CCC(NN=CC1=CC=CC(COC2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 48, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 48, 65, 65, 73, 73, 73, 73, 73, 48, 27, 8, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 1] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 19, 41, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 425 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086233 none CCC(NN=CC1=CC=CC(COC2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 165, 131, 64, 64, 19, 19, 19, 19, 19, 6, 2, 1, 1, 1, 1, 1, 1, 1, 19, 165, 201, 201, 201, 201, 201, 201, 201, 165, 131, 64, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 19] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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, 35, 41]) total number of confs: 917 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086233 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086233 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086233/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086233 Building REAL300000086234 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086234' /scratch/stefan/7769667/working/building/REAL300000086234 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086234 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086234/0 /scratch/stefan/7769667/working/building/REAL300000086234 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/247 `/scratch/stefan/7769667/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC2=C(Br)C=C(F)C=C2N1)C(=O)[O-]) `REAL300000086234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086234 none CCC(NN=CC1=CC2=C(Br)C=C(F)C=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 1, 15, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 36, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 39, 39, 45, 45, 45, 45, 45, 36, 21, 6, 1, 1, 1, 1] 45 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086234 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086234 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086234/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086234 Building REAL300000086235 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086235' /scratch/stefan/7769667/working/building/REAL300000086235 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086235 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086235/0 /scratch/stefan/7769667/working/building/REAL300000086235 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/248 `/scratch/stefan/7769667/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CCC1=CC=CC=C1)C1=CC=CN=C1)C(=O)[O-]) `REAL300000086235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086235 none CCC(NN=C(CCC1=CC=CC=C1)C1=CC=CN=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 123, 71, 22, 22, 5, 3, 1, 1, 1, 1, 1, 1, 1, 22, 73, 73, 73, 73, 73, 123, 157, 157, 166, 166, 166, 166, 166, 123, 71, 5, 5, 3, 3, 1, 1, 1, 1, 1, 73, 73, 73, 73] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39, 40, 41, 42]) total number of confs: 910 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086235 none CCC(NN=C(CCC1=CC=CC=C1)C1=CC=CN=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 70, 32, 7, 7, 1, 7, 56, 65, 73, 73, 65, 73, 73, 1, 1, 1, 1, 1, 1, 70, 97, 97, 105, 105, 105, 105, 105, 70, 32, 56, 56, 65, 65, 73, 73, 65, 73, 73, 1, 1, 1, 1] 201 rigid atoms, others: [5, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 822 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086235 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086235 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086235/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086235 Building REAL300000086236 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086236' /scratch/stefan/7769667/working/building/REAL300000086236 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086236 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086236/0 /scratch/stefan/7769667/working/building/REAL300000086236 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/249 `/scratch/stefan/7769667/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1)C(=O)[O-]) `REAL300000086236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086236 none CCC(NN=C(C)C1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [23, 17, 14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 9, 11, 11, 11, 17, 19, 19, 23, 23, 23, 23, 23, 17, 14, 7, 7, 7, 1, 1, 1, 11, 11, 11, 11] 32 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 126 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086236 none CCC(NN=C(C)C1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 30, 27, 19, 19, 11, 19, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 30, 32, 32, 32, 32, 32, 32, 32, 30, 27, 19, 19, 19, 11, 11, 11, 1, 1, 1, 1] 32 rigid atoms, others: [38, 39, 40, 41, 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, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086236 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086236 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086236/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086236 Building REAL300000086237 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086237' /scratch/stefan/7769667/working/building/REAL300000086237 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086237 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086237/0 /scratch/stefan/7769667/working/building/REAL300000086237 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/250 `/scratch/stefan/7769667/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=C([N+](=O)[O-])[N-]C(C(=O)OC)=C1)C(=O)[O-]) `REAL300000086237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086237 none CCC(NN=C(C)C1=C([N+](=O)[O-])[N-]C(C(=O)OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', '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, 5, 5, 8, 8, 1, 5, 1, 1, 8, 11, 11, 8, 1, 1, 11, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 5, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 11, 7, 7, 7, 3, 3, 3, 1] 16 rigid atoms, others: [35, 5, 7, 8, 9, 10, 11, 12, 13, 14, 18] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 62 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086237 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086237 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086237/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086237 Building REAL300000086238 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086238' /scratch/stefan/7769667/working/building/REAL300000086238 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086238 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086238/0 /scratch/stefan/7769667/working/building/REAL300000086238 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/251 `/scratch/stefan/7769667/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(Br)N=C2COCCN21)C(=O)[O-]) `REAL300000086238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086238 none CCC(NN=CC1=C(Br)N=C2COCCN21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', '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, 5, 5, 8, 8, 1, 1, 1, 17, 8, 1, 5, 12, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 38, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 40, 40, 52, 52, 52, 52, 52, 38, 25, 5, 1, 1, 1, 1, 1, 1] 52 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086238 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086238 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086238/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086238 Building REAL300000086239 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086239' /scratch/stefan/7769667/working/building/REAL300000086239 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086239 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086239/0 /scratch/stefan/7769667/working/building/REAL300000086239 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/252 `/scratch/stefan/7769667/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC2CC(C1)[N@H+](CC1=CC=CC=C1)C2)C(=O)[O-]) `REAL300000086239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086239 none CCC(NN=C1CC2CC(C1)[N@H+](CC1=CC=CC=C1)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 1, 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, 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: [11, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 3, 5, 5, 1, 8, 9, 9, 11, 11, 11, 11, 11, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 1, 1] 13 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086239 none CCC(NN=C1CC2CC(C1)[N@H+](CC1=CC=CC=C1)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 1, 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, 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, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 13, 13, 13, 13, 13, 13, 13, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 5, 5] 13 rigid atoms, others: [45, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) total number of confs: 58 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086239 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086239/1 /scratch/stefan/7769667/working/building/REAL300000086239 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/253 `/scratch/stefan/7769667/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC2CC(C1)[N@@H+](CC1=CC=CC=C1)C2)C(=O)[O-]) `REAL300000086239.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086239 none CCC(NN=C1CC2CC(C1)[N@@H+](CC1=CC=CC=C1)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 1, 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, 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 1, 1] 8 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 34 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086239 none CCC(NN=C1CC2CC(C1)[N@@H+](CC1=CC=CC=C1)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 1, 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, 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, 6, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 3, 3] 8 rigid atoms, others: [45, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) total number of confs: 31 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086239 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086239 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086239/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086239/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086239 Building REAL300000086240 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086240' /scratch/stefan/7769667/working/building/REAL300000086240 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086240 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086240/0 /scratch/stefan/7769667/working/building/REAL300000086240 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/254 `/scratch/stefan/7769667/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC(CC)C(=O)[O-])C1CN(C(=O)OC(C)(C)C)C1) `REAL300000086240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086240 none CCC(=NNC(CC)C(=O)[O-])C1CN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 5, 5, 1, 11, 11, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 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: [17, 7, 1, 7, 7, 28, 63, 89, 63, 84, 84, 1, 1, 1, 1, 2, 2, 9, 11, 11, 11, 1, 17, 17, 17, 17, 17, 28, 63, 89, 89, 89, 89, 89, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1] 201 rigid atoms, others: [34, 35, 36, 11, 12, 2, 14, 13, 21, 46, 47] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 559 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086240 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086240 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086240/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086240 Building REAL300000086241 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086241' /scratch/stefan/7769667/working/building/REAL300000086241 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086241 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086241/0 /scratch/stefan/7769667/working/building/REAL300000086241 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/255 `/scratch/stefan/7769667/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CN(C2CN(C(=O)OC(C)(C)C)C2)N=N1)C(=O)[O-]) `REAL300000086241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086241 none CCC(NN=C(C)C1=CN(C2CN(C(=O)OC(C)(C)C)C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 5, 1, 1, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 8, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 26, 13, 3, 3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 24, 24, 62, 66, 66, 66, 13, 1, 1, 26, 38, 38, 42, 42, 42, 42, 42, 26, 13, 4, 4, 4, 1, 13, 13, 13, 66, 66, 66, 66, 66, 66, 66, 66, 66, 13, 13] 201 rigid atoms, others: [36, 5, 7, 8, 9, 10, 21, 22] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 384 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086241 none CCC(NN=C(C)C1=CN(C2CN(C(=O)OC(C)(C)C)C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 5, 1, 1, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 8, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 87, 65, 26, 26, 13, 26, 13, 13, 1, 1, 1, 1, 1, 3, 3, 10, 12, 12, 12, 1, 13, 13, 87, 98, 98, 103, 103, 103, 103, 103, 87, 65, 26, 26, 26, 13, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1] 201 rigid atoms, others: [37, 38, 39, 9, 10, 11, 12, 13, 49, 50, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 452 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086241 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086241 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086241/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086241 Building REAL300000086242 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086242' /scratch/stefan/7769667/working/building/REAL300000086242 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086242 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086242/0 /scratch/stefan/7769667/working/building/REAL300000086242 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/256 `/scratch/stefan/7769667/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN1C=C(C=NNC(CC)C(=O)[O-])C(C2=CC=CN=C2)=N1) `REAL300000086242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086242 none CCOC(=O)CN1C=C(C=NNC(CC)C(=O)[O-])C(C2=CC=CN=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 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: [73, 46, 40, 6, 40, 1, 1, 1, 1, 1, 4, 4, 8, 14, 18, 14, 18, 18, 1, 1, 7, 7, 7, 7, 7, 1, 73, 73, 73, 73, 73, 6, 6, 1, 4, 8, 14, 18, 18, 18, 18, 18, 7, 7, 7, 7] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 18, 19, 25] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 356 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086242 none CCOC(=O)CN1C=C(C=NNC(CC)C(=O)[O-])C(C2=CC=CN=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 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: [141, 114, 107, 25, 107, 7, 7, 7, 7, 7, 10, 10, 21, 33, 38, 33, 38, 38, 1, 1, 1, 1, 1, 1, 1, 7, 141, 141, 141, 141, 141, 25, 25, 7, 10, 21, 33, 38, 38, 38, 38, 38, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 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, 40, 41]) total number of confs: 616 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086242 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086242 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086242/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086242 Building REAL300000086243 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086243' /scratch/stefan/7769667/working/building/REAL300000086243 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086243 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086243/0 /scratch/stefan/7769667/working/building/REAL300000086243 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/257 `/scratch/stefan/7769667/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN1C=C(C=NNC(CC)C(=O)[O-])C(C2=CN(C)N=C2)=N1) `REAL300000086243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086243 none CCOC(=O)CN1C=C(C=NNC(CC)C(=O)[O-])C(C2=CN(C)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 8, 5, 8, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 40, 6, 40, 1, 1, 1, 1, 1, 4, 4, 11, 17, 24, 17, 21, 21, 1, 1, 7, 7, 7, 7, 7, 1, 68, 68, 68, 68, 68, 6, 6, 1, 4, 11, 17, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 18, 19, 25] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086243 none CCOC(=O)CN1C=C(C=NNC(CC)C(=O)[O-])C(C2=CN(C)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 8, 5, 8, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 92, 91, 21, 91, 7, 7, 7, 7, 7, 9, 9, 19, 28, 38, 28, 34, 34, 1, 1, 1, 1, 1, 1, 1, 7, 124, 124, 124, 124, 124, 21, 21, 7, 9, 19, 28, 38, 38, 38, 38, 38, 1, 2, 2, 2, 1] 201 rigid atoms, others: [42, 46, 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, 40, 41, 43, 44, 45]) total number of confs: 609 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086243 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086243 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086243/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086243 Building REAL300000086244 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086244' /scratch/stefan/7769667/working/building/REAL300000086244 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086244 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086244/0 /scratch/stefan/7769667/working/building/REAL300000086244 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/258 `/scratch/stefan/7769667/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CC1CN(C(=O)OC(C)(C)C)C1)C(C)C)C(=O)[O-]) `REAL300000086244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086244 none CCC(NN=C(CC1CN(C(=O)OC(C)(C)C)C1)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 82, 53, 17, 17, 5, 1, 1, 1, 1, 1, 3, 3, 10, 12, 12, 12, 1, 17, 30, 30, 82, 95, 95, 96, 96, 96, 96, 96, 82, 53, 5, 5, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 30, 30, 30, 30, 30, 30, 30] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 45, 46, 17] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 550 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086244 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086244 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086244/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086244 Building REAL300000086245 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086245' /scratch/stefan/7769667/working/building/REAL300000086245 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086245 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086245/0 /scratch/stefan/7769667/working/building/REAL300000086245 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/259 `/scratch/stefan/7769667/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=C(Br)S1)C(=O)[O-]) `REAL300000086245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086245 none CCC(NN=CC1=CC(Br)=C(Br)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'Br', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 17, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [72, 54, 32, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 54, 58, 58, 72, 72, 72, 72, 72, 54, 32, 6, 1] 73 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 24] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 315 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086245 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086245 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086245/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086245 Building REAL300000086246 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086246' /scratch/stefan/7769667/working/building/REAL300000086246 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086246 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086246/0 /scratch/stefan/7769667/working/building/REAL300000086246 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/260 `/scratch/stefan/7769667/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1OC1=CC=C(Br)C=C1F)C(=O)[O-]) `REAL300000086246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086246 none CCC(NN=CC1=CC=CC=C1OC1=CC=C(Br)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'Br', 'C.ar', 'C.ar', 'F', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [23, 12, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 9, 22, 22, 22, 22, 12, 15, 15, 23, 23, 23, 23, 23, 12, 8, 4, 1, 1, 1, 1, 22, 22, 22] 73 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12] 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, 36, 37, 38]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086246 none CCC(NN=CC1=CC=CC=C1OC1=CC=C(Br)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'Br', 'C.ar', 'C.ar', 'F', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 64, 43, 30, 30, 22, 22, 22, 22, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 64, 73, 73, 73, 73, 73, 73, 73, 64, 43, 30, 22, 22, 22, 22, 1, 1, 1] 73 rigid atoms, others: [36, 37, 38, 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: 302 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086246 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086246 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086246/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086246 Building REAL300000086247 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086247' /scratch/stefan/7769667/working/building/REAL300000086247 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086247 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086247/0 /scratch/stefan/7769667/working/building/REAL300000086247 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/261 `/scratch/stefan/7769667/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(F)C(Cl)=C1)C(=O)[O-]) `REAL300000086247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086247 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(F)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', '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, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [16, 13, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 30, 30, 30, 30, 30, 30, 30, 13, 16, 16, 16, 16, 16, 16, 16, 13, 8, 4, 1, 1, 1, 30, 30, 30] 134 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 110 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086247 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(F)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', '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, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 123, 68, 45, 45, 30, 30, 30, 30, 30, 30, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 123, 134, 134, 134, 134, 134, 134, 134, 123, 68, 45, 30, 29, 30, 1, 1, 1] 134 rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 569 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086247 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086247 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086247/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086247 Building REAL300000086248 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086248' /scratch/stefan/7769667/working/building/REAL300000086248 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086248 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086248/0 /scratch/stefan/7769667/working/building/REAL300000086248 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/262 `/scratch/stefan/7769667/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(F)=CC=C1OC1=CC(F)=CC(F)=C1)C(=O)[O-]) `REAL300000086248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086248 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC(F)=CC(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 6, 10, 10, 10, 7, 7, 7, 8, 8, 8, 8, 8, 7, 6, 4, 1, 1, 1, 10, 7, 10] 23 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086248 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC(F)=CC(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 66, 36, 23, 23, 16, 16, 16, 15, 15, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 72, 72, 72, 72, 72, 72, 72, 66, 36, 23, 16, 16, 16, 1, 1, 1] 72 rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 307 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086248 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086248 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086248/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086248 Building REAL300000086249 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086249' /scratch/stefan/7769667/working/building/REAL300000086249 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086249 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086249/0 /scratch/stefan/7769667/working/building/REAL300000086249 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/263 `/scratch/stefan/7769667/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(Br)C=C1OC1=CC=C(C)C=C1)C(=O)[O-]) `REAL300000086249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086249 none CCC(NN=CC1=CC=C(Br)C=C1OC1=CC=C(C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 9, 8, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9] 24 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086249 none CCC(NN=CC1=CC=C(Br)C=C1OC1=CC=C(C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 22, 13, 13, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 22, 13, 9, 9, 9, 1, 1, 2, 2, 2, 1, 1] 24 rigid atoms, others: [35, 36, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086249 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086249 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086249/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086249 Building REAL300000086250 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086250' /scratch/stefan/7769667/working/building/REAL300000086250 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086250 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086250/0 /scratch/stefan/7769667/working/building/REAL300000086250 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/264 `/scratch/stefan/7769667/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Cl)=CC=C1OC1=CC=C(Cl)C=C1)C(=O)[O-]) `REAL300000086250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086250 none CCC(NN=CC1=CC(Cl)=CC=C1OC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 9, 9, 9, 12, 12, 12, 12, 12, 9, 7, 4, 1, 1, 1, 8, 8, 8, 8] 21 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086250 none CCC(NN=CC1=CC(Cl)=CC=C1OC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 19, 12, 12, 8, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 12, 8, 8, 8, 1, 1, 1, 1] 21 rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086250 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086250 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086250/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086250 Building REAL300000086251 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086251' /scratch/stefan/7769667/working/building/REAL300000086251 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086251 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086251/0 /scratch/stefan/7769667/working/building/REAL300000086251 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/265 `/scratch/stefan/7769667/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1OC1=CC=C(C)C=C1OC)C(=O)[O-]) `REAL300000086251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086251 none CCC(NN=CC1=CC=CC=C1OC1=CC=C(C)C=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [23, 11, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 15, 22, 22, 22, 22, 39, 11, 16, 16, 23, 23, 23, 23, 23, 11, 8, 4, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 39, 39, 39] 107 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12] 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, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 208 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086251 none CCC(NN=CC1=CC=CC=C1OC1=CC=C(C)C=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [102, 68, 42, 28, 28, 22, 22, 22, 22, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 68, 88, 88, 102, 102, 102, 102, 102, 68, 42, 28, 22, 22, 22, 22, 1, 1, 2, 2, 2, 1, 4, 4, 4] 107 rigid atoms, others: [37, 38, 42, 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, 39, 40, 41, 43, 44, 45]) total number of confs: 503 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086251 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086251 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086251/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086251 Building REAL300000086252 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086252' /scratch/stefan/7769667/working/building/REAL300000086252 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086252 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086252/0 /scratch/stefan/7769667/working/building/REAL300000086252 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/266 `/scratch/stefan/7769667/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300000086252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086252 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 6, 6, 8, 8, 9, 9, 9, 13, 13, 13, 13, 13, 9, 7, 4, 1, 1, 1, 8, 8, 8, 8] 22 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086252 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 20, 13, 13, 8, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 20, 13, 8, 8, 8, 1, 1, 1, 1] 22 rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086252 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086252 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086252/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086252 Building REAL300000086253 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086253' /scratch/stefan/7769667/working/building/REAL300000086253 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086253 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086253/0 /scratch/stefan/7769667/working/building/REAL300000086253 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/267 `/scratch/stefan/7769667/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1)C(=O)[O-]) `REAL300000086253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086253 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 6, 8, 8, 8, 9, 9, 9, 12, 12, 12, 12, 12, 9, 7, 4, 1, 1, 1, 8, 8, 8, 8] 21 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086253 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 19, 12, 12, 8, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 12, 8, 8, 8, 1, 1, 1, 1] 21 rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086253 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086253 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086253/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086253 Building REAL300000086254 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086254' /scratch/stefan/7769667/working/building/REAL300000086254 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086254 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086254/0 /scratch/stefan/7769667/working/building/REAL300000086254 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/268 `/scratch/stefan/7769667/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1OC1=CC(Cl)=CC(Cl)=C1)C(=O)[O-]) `REAL300000086254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086254 none CCC(NN=CC1=CC=CC=C1OC1=CC(Cl)=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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, 8, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 7, 11, 11, 11, 8, 8, 8, 10, 10, 10, 10, 10, 8, 7, 4, 1, 1, 1, 1, 11, 7, 11] 22 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12] 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, 36, 37, 38]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086254 none CCC(NN=CC1=CC=CC=C1OC1=CC(Cl)=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 58, 34, 21, 21, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 62, 62, 62, 62, 62, 62, 62, 58, 34, 21, 17, 17, 17, 17, 1, 1, 1] 62 rigid atoms, others: [36, 37, 38, 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: 230 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086254 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086254 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086254/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086254 Building REAL300000086255 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086255' /scratch/stefan/7769667/working/building/REAL300000086255 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086255 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086255/0 /scratch/stefan/7769667/working/building/REAL300000086255 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/269 `/scratch/stefan/7769667/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(F)C=C1Cl)C(=O)[O-]) `REAL300000086255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086255 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(F)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [19, 14, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 13, 14, 15, 15, 15, 14, 16, 16, 19, 19, 19, 19, 19, 14, 9, 4, 1, 1, 1, 15, 15, 15] 45 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086255 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(F)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 43, 26, 19, 19, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 45, 45, 45, 45, 45, 45, 45, 43, 26, 19, 15, 15, 15, 1, 1, 1] 45 rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 170 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086255 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086255 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086255/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086255 Building REAL300000086256 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086256' /scratch/stefan/7769667/working/building/REAL300000086256 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086256 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086256/0 /scratch/stefan/7769667/working/building/REAL300000086256 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/270 `/scratch/stefan/7769667/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(SC)C=C1)C(=O)[O-]) `REAL300000086256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086256 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(SC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 14, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 36, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 16, 16, 12, 16, 65, 16, 16, 36, 53, 53, 56, 56, 56, 56, 56, 36, 19, 6, 1, 1, 1, 16, 16, 65, 65, 65, 16, 16] 201 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 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: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086256 none CCC(NN=CC1=CC(F)=CC=C1OC1=CC=C(SC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 14, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 127, 78, 36, 36, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 127, 146, 146, 158, 158, 158, 158, 158, 127, 78, 36, 16, 16, 16, 1, 1, 11, 11, 11, 1, 1] 201 rigid atoms, others: [36, 37, 41, 42, 13, 14, 15, 16, 17, 18, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 736 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086256 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086256 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086256/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086256 Building REAL300000086257 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086257' /scratch/stefan/7769667/working/building/REAL300000086257 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086257 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086257/0 /scratch/stefan/7769667/working/building/REAL300000086257 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/271 `/scratch/stefan/7769667/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(Cl)C=C1OC1=CC=C(F)C(Cl)=C1)C(=O)[O-]) `REAL300000086257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086257 none CCC(NN=CC1=CC=C(Cl)C=C1OC1=CC=C(F)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [20, 13, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 31, 31, 31, 31, 31, 31, 31, 13, 16, 16, 20, 20, 20, 20, 20, 13, 8, 4, 1, 1, 1, 31, 31, 31] 140 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 135 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086257 none CCC(NN=CC1=CC=C(Cl)C=C1OC1=CC=C(F)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 130, 67, 44, 44, 31, 31, 31, 15, 31, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 130, 140, 140, 140, 140, 140, 140, 140, 130, 67, 44, 31, 31, 31, 1, 1, 1] 140 rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 637 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086257 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086257 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086257/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086257 Building REAL300000086258 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086258' /scratch/stefan/7769667/working/building/REAL300000086258 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086258 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086258/0 /scratch/stefan/7769667/working/building/REAL300000086258 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/272 `/scratch/stefan/7769667/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C)N(C2=CC=CC=C2C)N=C1C)C(=O)[O-]) `REAL300000086258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086258 none CCC(NN=CC1=C(C)N(C2=CC=CC=C2C)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 5, 1, 11, 11, 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, 4, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 11, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 3, 1, 1, 1, 13, 13, 13, 14, 14, 14, 14, 14, 13, 10, 6, 2, 2, 2, 3, 3, 1, 3, 3, 3, 3, 2, 2, 2] 26 rigid atoms, others: [5, 6, 7, 8, 9, 10, 17, 18, 19] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 20, 21, 22, 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: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086258 none CCC(NN=CC1=C(C)N(C2=CC=CC=C2C)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 5, 1, 11, 11, 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, 4, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 20, 13, 13, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 24, 24, 24, 26, 26, 26, 26, 26, 24, 20, 13, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3] 26 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086258 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086258 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086258/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086258 Building REAL300000086259 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086259' /scratch/stefan/7769667/working/building/REAL300000086259 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086259 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086259/0 /scratch/stefan/7769667/working/building/REAL300000086259 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/273 `/scratch/stefan/7769667/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=CC=C1SC(F)(F)F)C(=O)[O-]) `REAL300000086259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086259 none CCC(NN=C(C)C1=CC=CC=C1SC(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens 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, 78, 37, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 78, 110, 110, 122, 122, 122, 122, 122, 78, 37, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 702 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086259 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086259 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086259/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086259 Building REAL300000086260 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086260' /scratch/stefan/7769667/working/building/REAL300000086260 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086260 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086260/0 /scratch/stefan/7769667/working/building/REAL300000086260 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/274 `/scratch/stefan/7769667/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Cl)=C(OC(C)C(=O)[O-])C(OC)=C1)C(=O)[O-]) `REAL300000086260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086260 none CCC(NN=CC1=CC(Cl)=C(OC(C)C(=O)[O-])C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 16, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [83, 53, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 20, 20, 1, 1, 3, 1, 53, 78, 78, 83, 83, 83, 83, 83, 53, 27, 7, 1, 13, 14, 13, 14, 4, 4, 4, 1] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 17, 18, 20, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 535 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086260 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086260 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086260/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086260 Building REAL300000086261 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086261' /scratch/stefan/7769667/working/building/REAL300000086261 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086261 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086261/0 /scratch/stefan/7769667/working/building/REAL300000086261 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/275 `/scratch/stefan/7769667/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CS(=O)(=O)N2CC(OC)CC12C)C(=O)[O-]) `REAL300000086261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 Warning: OE3DToAtomStereo is unable to perceive atom stereo from a flat geometry on atom 10 of molecule 'REAL300000086261' Warning: REAL300000086261 failed due to unspecified stereochemistry with strict stereo enabled ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] Conformer generation failed Skipping REAL300000086261 0 /scratch/stefan/7769667/working/building/REAL300000086261 /scratch/stefan/7769667/working /scratch/stefan/7769667 `0' -> `0.failed' Finished preparing REAL300000086261 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Found failed protomers Marking REAL300000086261 as failed mkdir: created directory `/scratch/stefan/7769667/failed' `/scratch/stefan/7769667/working/building/REAL300000086261' -> `/scratch/stefan/7769667/failed/REAL300000086261' Building REAL300000086262 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086262' /scratch/stefan/7769667/working/building/REAL300000086262 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086262 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086262/0 /scratch/stefan/7769667/working/building/REAL300000086262 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/276 `/scratch/stefan/7769667/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=NC(C)=C(Br)S1)C(=O)[O-]) `REAL300000086262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086262 none CCC(NN=CC1=NC(C)=C(Br)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'Br', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 5, 1, 17, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [63, 46, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 46, 48, 48, 63, 63, 63, 63, 63, 46, 30, 7, 2, 2, 2] 64 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086262 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086262 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086262/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086262 Building REAL300000086263 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086263' /scratch/stefan/7769667/working/building/REAL300000086263 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086263 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086263/0 /scratch/stefan/7769667/working/building/REAL300000086263 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/277 `/scratch/stefan/7769667/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC2=CC=CC=C2C(OC)=C1)C(=O)[O-]) `REAL300000086263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086263 none CCC(NN=C(C)C1=CC2=CC=CC=C2C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 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: [127, 94, 47, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 94, 119, 119, 127, 127, 127, 127, 127, 94, 47, 12, 12, 12, 1, 1, 1, 1, 1, 4, 4, 4, 1] 140 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 18] set([0, 1, 2, 3, 4, 6, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 636 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086263 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086263 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086263/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086263 Building REAL300000086264 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086264' /scratch/stefan/7769667/working/building/REAL300000086264 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086264 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086264/0 /scratch/stefan/7769667/working/building/REAL300000086264 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/278 `/scratch/stefan/7769667/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(OC2=CC=C(F)C=C2)=C1)C(=O)[O-]) `REAL300000086264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086264 none CCC(NN=CC1=CC=CC(OC2=CC=C(F)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 32, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 32, 40, 40, 46, 46, 46, 46, 46, 32, 21, 8, 1, 1, 1, 19, 19, 19, 19, 1] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 19, 38, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086264 none CCC(NN=CC1=CC=CC(OC2=CC=C(F)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 182, 169, 100, 100, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 182, 201, 201, 201, 201, 201, 201, 201, 182, 169, 100, 19, 19, 19, 1, 1, 1, 1, 19] 201 rigid atoms, others: [34, 35, 36, 37, 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, 33, 38]) total number of confs: 719 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086264 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086264 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086264/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086264 Building REAL300000086265 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086265' /scratch/stefan/7769667/working/building/REAL300000086265 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086265 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086265/0 /scratch/stefan/7769667/working/building/REAL300000086265 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/279 `/scratch/stefan/7769667/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1)C(=O)[O-]) `REAL300000086265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086265 none CCC(NN=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1)C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [18, 14, 8, 5, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 11, 11, 10, 1, 14, 15, 15, 18, 18, 18, 18, 18, 14, 8, 5, 1, 1, 10, 10, 20, 10] 58 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 20] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086265 none CCC(NN=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1)C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [29, 28, 22, 18, 18, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 10, 28, 29, 29, 29, 29, 29, 29, 29, 28, 22, 18, 10, 10, 1, 1, 2, 1] 58 rigid atoms, others: [34, 35, 37, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086265 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086265 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086265/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086265 Building REAL300000086266 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086266' /scratch/stefan/7769667/working/building/REAL300000086266 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086266 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086266/0 /scratch/stefan/7769667/working/building/REAL300000086266 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/280 `/scratch/stefan/7769667/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C2=CC=C(F)C=C2)N=C2C=CC(F)=CN21)C(=O)[O-]) `REAL300000086266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086266 none CCC(NN=CC1=C(C2=CC=C(F)C=C2)N=C2C=CC(F)=CN21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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] 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: [24, 17, 12, 4, 4, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 17, 21, 21, 24, 24, 24, 24, 24, 17, 12, 4, 4, 4, 4, 4, 1, 1, 1] 25 rigid atoms, others: [5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 40, 39, 38] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086266 none CCC(NN=CC1=C(C2=CC=C(F)C=C2)N=C2C=CC(F)=CN21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 16, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 21, 25, 25, 25, 25, 25, 25, 25, 21, 16, 7, 1, 1, 1, 1, 4, 4, 4] 25 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086266 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086266 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086266/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086266 Building REAL300000086267 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086267' /scratch/stefan/7769667/working/building/REAL300000086267 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086267 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086267/0 /scratch/stefan/7769667/working/building/REAL300000086267 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/281 `/scratch/stefan/7769667/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=CC(S(=O)(=O)C(F)(F)F)=C1)C(=O)[O-]) `REAL300000086267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086267 none CCC(NN=C(C)C1=CC=CC(S(=O)(=O)C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'F', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [79, 68, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 1, 68, 74, 74, 79, 79, 79, 79, 79, 68, 37, 11, 11, 11, 1, 1, 1, 1] 92 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 19] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 354 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086267 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086267 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086267/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086267 Building REAL300000086268 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086268' /scratch/stefan/7769667/working/building/REAL300000086268 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086268 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086268/0 /scratch/stefan/7769667/working/building/REAL300000086268 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/282 `/scratch/stefan/7769667/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=C(I)C2=CC=CC=C2C=C1)C(=O)[O-]) `REAL300000086268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086268 none CCC(NN=C(C)C1=C(I)C2=CC=CC=C2C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 40, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 41, 41, 43, 43, 43, 43, 43, 40, 26, 7, 7, 7, 1, 1, 1, 1, 1, 1] 43 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 159 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086268 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086268 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086268/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086268 Building REAL300000086269 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086269' /scratch/stefan/7769667/working/building/REAL300000086269 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086269 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086269/0 /scratch/stefan/7769667/working/building/REAL300000086269 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/283 `/scratch/stefan/7769667/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=CC=C1Br)C(=O)[O-]) `REAL300000086269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086269 none CCC(NN=CC1=CC(Br)=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 42, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 53, 53, 53, 53, 53, 42, 27, 9, 1, 1, 1] 53 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086269 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086269 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086269/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086269 Building REAL300000086270 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086270' /scratch/stefan/7769667/working/building/REAL300000086270 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086270 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086270/0 /scratch/stefan/7769667/working/building/REAL300000086270 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/284 `/scratch/stefan/7769667/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C)=C(I)C=C1C)C(=O)[O-]) `REAL300000086270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086270 none CCC(NN=CC1=CC(C)=C(I)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'I', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 5, 1, 18, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 48, 35, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 51, 51, 63, 63, 63, 63, 63, 48, 35, 11, 1, 2, 2, 2, 1, 2, 2, 2] 63 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 30] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33]) total number of confs: 271 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086270 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086270 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086270/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086270 Building REAL300000086271 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086271' /scratch/stefan/7769667/working/building/REAL300000086271 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086271 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086271/0 /scratch/stefan/7769667/working/building/REAL300000086271 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/285 `/scratch/stefan/7769667/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C#N)=CC=C1Br)C(=O)[O-]) `REAL300000086271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086271 none CCC(NN=CC1=CC(C#N)=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 45, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 46, 46, 57, 57, 57, 57, 57, 45, 33, 9, 1, 1, 1] 57 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086271 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086271 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086271/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086271 Building REAL300000086272 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086272' /scratch/stefan/7769667/working/building/REAL300000086272 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086272 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086272/0 /scratch/stefan/7769667/working/building/REAL300000086272 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/286 `/scratch/stefan/7769667/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1OC(C)C(=O)OC)C(=O)[O-]) `REAL300000086272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086272 none CCC(NN=CC1=CC=CC=C1OC(C)C(=O)OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 5, 3, 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 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [30, 16, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 48, 48, 48, 16, 23, 23, 30, 30, 30, 30, 30, 16, 8, 4, 1, 1, 1, 1, 22, 22, 22, 22, 48, 48, 48] 141 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 312 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086272 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086272 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086272/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086272 Building REAL300000086273 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086273' /scratch/stefan/7769667/working/building/REAL300000086273 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086273 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086273/0 /scratch/stefan/7769667/working/building/REAL300000086273 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/287 `/scratch/stefan/7769667/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCCC2=CC=C(OC)C(Cl)=C21)C(=O)[O-]) `REAL300000086273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086273 none CCC(NN=C1CCCC2=CC=C(OC)C(Cl)=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [29, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 19, 27, 27, 29, 29, 29, 29, 29, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4] 34 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 2, 36, 37, 38, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 164 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086273 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086273 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086273/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086273 Building REAL300000086274 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086274' /scratch/stefan/7769667/working/building/REAL300000086274 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086274 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086274/0 /scratch/stefan/7769667/working/building/REAL300000086274 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/288 `/scratch/stefan/7769667/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC2(C1)CCN(C(=O)OC(C)(C)C)CC2)C(=O)[O-]) `REAL300000086274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086274 none CCC(NN=C1CC2(C1)CCN(C(=O)OC(C)(C)C)CC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 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: [38, 24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 22, 22, 22, 1, 1, 24, 33, 33, 38, 38, 38, 38, 38, 24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1] 89 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086274 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086274 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086274/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086274 Building REAL300000086275 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086275' /scratch/stefan/7769667/working/building/REAL300000086275 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086275 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086275/0 /scratch/stefan/7769667/working/building/REAL300000086275 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/289 `/scratch/stefan/7769667/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCCC2=NC=C(Br)C=C12)C(=O)[O-]) `REAL300000086275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086275 none CCC(NN=C1CCCC2=NC=C(Br)C=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [25, 17, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 19, 19, 25, 25, 25, 25, 25, 17, 8, 1, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 112 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086275 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086275 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086275/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086275 Building REAL300000086276 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086276' /scratch/stefan/7769667/working/building/REAL300000086276 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086276 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086276/0 /scratch/stefan/7769667/working/building/REAL300000086276 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/290 `/scratch/stefan/7769667/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCOC2(CCN(C(=O)OC(C)(C)C)CC2)C1)C(=O)[O-]) `REAL300000086276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086276 none CCC(NN=C1CCOC2(CCN(C(=O)OC(C)(C)C)CC2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 3, 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, 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: [40, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 1, 1, 1, 25, 36, 36, 40, 40, 40, 40, 40, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 20, 20, 20, 21, 21, 21, 1, 1, 1, 1, 1, 1] 93 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 253 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086276 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086276 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086276/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086276 Building REAL300000086277 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086277' /scratch/stefan/7769667/working/building/REAL300000086277 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086277 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086277/0 /scratch/stefan/7769667/working/building/REAL300000086277 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/291 `/scratch/stefan/7769667/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC(CNC(=O)OC(C)(C)C)C1)C(=O)[O-]) `REAL300000086277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086277 none CCC(NN=C1CCC(CNC(=O)OC(C)(C)C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 1, 1, 1, 1, 1, 1, 1, 8, 35, 62, 62, 79, 79, 79, 79, 1, 16, 24, 24, 26, 26, 26, 26, 26, 16, 6, 1, 1, 1, 1, 1, 8, 8, 35, 79, 79, 79, 79, 79, 79, 79, 79, 79, 1, 1] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 46, 47, 18, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086277 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086277 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086277/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086277 Building REAL300000086278 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086278' /scratch/stefan/7769667/working/building/REAL300000086278 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086278 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086278/0 /scratch/stefan/7769667/working/building/REAL300000086278 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/292 `/scratch/stefan/7769667/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1OC1=CC=CC(F)=C1)C(=O)[O-]) `REAL300000086278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086278 none CCC(NN=CC1=CC=CC=C1OC1=CC=CC(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [21, 12, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 31, 31, 31, 31, 31, 31, 12, 15, 15, 21, 21, 21, 21, 21, 12, 9, 4, 1, 1, 1, 1, 31, 31, 31, 31] 107 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]) total number of confs: 134 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086278 none CCC(NN=CC1=CC=CC=C1OC1=CC=CC(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 96, 59, 40, 40, 31, 31, 31, 30, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 96, 100, 100, 107, 107, 107, 107, 107, 96, 59, 40, 31, 30, 31, 31, 1, 1, 1, 1] 107 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]) total number of confs: 402 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086278 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086278 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086278/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086278 Building REAL300000086279 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086279' /scratch/stefan/7769667/working/building/REAL300000086279 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086279 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086279/0 /scratch/stefan/7769667/working/building/REAL300000086279 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/293 `/scratch/stefan/7769667/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C)C=CC(OC)=C1Br)C(=O)[O-]) `REAL300000086279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086279 none CCC(NN=CC1=C(C)C=CC(OC)=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Br', '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, 5, 5, 8, 8, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 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: [60, 43, 28, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 43, 56, 56, 60, 60, 60, 60, 60, 43, 28, 10, 2, 2, 2, 1, 1, 4, 4, 4] 94 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086279 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086279 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086279/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086279 Building REAL300000086280 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086280' /scratch/stefan/7769667/working/building/REAL300000086280 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086280 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086280/0 /scratch/stefan/7769667/working/building/REAL300000086280 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/294 `/scratch/stefan/7769667/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(OC2=CC=C(F)C=C2)C=C1)C(=O)[O-]) `REAL300000086280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086280 none CCC(NN=C(C)C1=CC=C(OC2=CC=C(F)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', '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', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 49, 25, 6, 6, 1, 6, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 1, 49, 61, 61, 66, 66, 66, 66, 66, 49, 25, 6, 6, 6, 1, 1, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 40, 19, 20, 41] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 353 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086280 none CCC(NN=C(C)C1=CC=C(OC2=CC=C(F)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', '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', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 149, 69, 69, 8, 69, 5, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 197, 201, 201, 201, 201, 201, 201, 201, 197, 149, 69, 69, 69, 19, 19, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [36, 37, 38, 39, 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, 33, 34, 35, 40, 41]) total number of confs: 774 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086280 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086280 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086280/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086280 Building REAL300000086281 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086281' /scratch/stefan/7769667/working/building/REAL300000086281 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086281 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086281/0 /scratch/stefan/7769667/working/building/REAL300000086281 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/295 `/scratch/stefan/7769667/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(C(=O)N(CC)CC)C=C1)C(=O)[O-]) `REAL300000086281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086281 none CCC(NN=CC1=CC=C(C(=O)N(CC)CC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 51, 23, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 11, 20, 11, 16, 1, 1, 51, 71, 71, 77, 77, 77, 77, 77, 51, 23, 5, 1, 1, 20, 20, 20, 20, 20, 16, 16, 16, 16, 16, 1, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 43, 17, 18, 42, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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: 516 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086281 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086281 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086281/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086281 Building REAL300000086282 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086282' /scratch/stefan/7769667/working/building/REAL300000086282 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086282 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086282/0 /scratch/stefan/7769667/working/building/REAL300000086282 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/296 `/scratch/stefan/7769667/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC(C)(CNC(=O)OC(C)(C)C)CC1)C(=O)[O-]) `REAL300000086282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086282 none CCC(NN=C1CCC(C)(CNC(=O)OC(C)(C)C)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 8, 35, 60, 60, 66, 66, 66, 66, 1, 1, 18, 26, 26, 28, 28, 28, 28, 28, 18, 7, 1, 1, 1, 1, 2, 2, 2, 8, 8, 35, 66, 66, 66, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 50, 19, 20, 53, 52, 51, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 367 number of broken/clashed sets: 107 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086282 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086282 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086282/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086282 Building REAL300000086283 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086283' /scratch/stefan/7769667/working/building/REAL300000086283 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086283 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086283/0 /scratch/stefan/7769667/working/building/REAL300000086283 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/297 `/scratch/stefan/7769667/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C(=O)NC2=CC=C(Cl)C(Cl)=C21)C(=O)[O-]) `REAL300000086283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086283 none CCC(NN=C1C(=O)NC2=CC=C(Cl)C(Cl)=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 16, 16, 16, 16, 16, 14, 5, 1, 1, 1] 16 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29] set([0, 1, 2, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086283 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086283 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086283/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086283 Building REAL300000086284 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086284' /scratch/stefan/7769667/working/building/REAL300000086284 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086284 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086284/0 /scratch/stefan/7769667/working/building/REAL300000086284 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/298 `/scratch/stefan/7769667/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=C(C)C2=CC=CC(C)=C2S1)C(=O)[O-]) `REAL300000086284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086284 none CCC(NN=C(C)C1=C(C)C2=CC=CC(C)=C2S1)C(=O)[O-] 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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 5, 1, 1, 1, 1, 1, 5, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 63, 43, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 66, 66, 70, 70, 70, 70, 70, 63, 42, 10, 10, 10, 2, 2, 2, 1, 1, 1, 2, 2, 2] 70 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 287 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086284 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086284 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086284/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086284 Building REAL300000086285 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086285' /scratch/stefan/7769667/working/building/REAL300000086285 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086285 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086285/0 /scratch/stefan/7769667/working/building/REAL300000086285 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/299 `/scratch/stefan/7769667/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1)C(=O)[O-]) `REAL300000086285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086285 none CCC(NN=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1)C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 2, 2, 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: [49, 31, 17, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 12, 1, 31, 38, 38, 49, 49, 49, 49, 49, 31, 16, 6, 1, 1, 12, 12, 12, 12] 95 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 19, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086285 none CCC(NN=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1)C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 87, 68, 41, 41, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 87, 95, 95, 95, 95, 95, 95, 95, 87, 68, 41, 12, 12, 1, 1, 1, 1] 95 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 376 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086285 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086285 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086285/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086285 Building REAL300000086286 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086286' /scratch/stefan/7769667/working/building/REAL300000086286 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086286 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086286/0 /scratch/stefan/7769667/working/building/REAL300000086286 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/300 `/scratch/stefan/7769667/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=C(C)C2=CC(C)=CC(C)=C2S1)C(=O)[O-]) `REAL300000086286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086286 none CCC(NN=C(C)C1=C(C)C2=CC(C)=CC(C)=C2S1)C(=O)[O-] 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.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 5, 1, 1, 1, 5, 1, 1, 5, 1, 14, 1, 11, 11, 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, 4, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 59, 41, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 63, 63, 68, 68, 68, 68, 68, 59, 40, 10, 10, 10, 2, 2, 2, 1, 2, 2, 2, 1, 2, 2, 2] 68 rigid atoms, others: [35, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 39] set([0, 1, 2, 3, 4, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 40, 41, 42]) total number of confs: 293 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086286 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086286 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086286/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086286 Building REAL300000086287 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086287' /scratch/stefan/7769667/working/building/REAL300000086287 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086287 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086287/0 /scratch/stefan/7769667/working/building/REAL300000086287 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/301 `/scratch/stefan/7769667/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C(=O)NC2=C1C=C(F)C(F)=C2Br)C(=O)[O-]) `REAL300000086287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086287 none CCC(NN=C1C(=O)NC2=C1C=C(F)C(F)=C2Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 17, 17, 19, 19, 19, 19, 19, 16, 6, 1, 1] 19 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29] set([0, 1, 2, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086287 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086287 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086287/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086287 Building REAL300000086288 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086288' /scratch/stefan/7769667/working/building/REAL300000086288 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086288 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086288/0 /scratch/stefan/7769667/working/building/REAL300000086288 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/302 `/scratch/stefan/7769667/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=C(C)C2=CC=CC(Cl)=C2S1)C(=O)[O-]) `REAL300000086288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086288 none CCC(NN=C(C)C1=C(C)C2=CC=CC(Cl)=C2S1)C(=O)[O-] 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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.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, 5, 5, 8, 8, 1, 5, 1, 1, 5, 1, 1, 1, 1, 1, 16, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 63, 42, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 67, 67, 71, 71, 71, 71, 71, 63, 41, 10, 10, 10, 2, 2, 2, 1, 1, 1] 71 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 293 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086288 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086288 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086288/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086288 Building REAL300000086289 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086289' /scratch/stefan/7769667/working/building/REAL300000086289 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086289 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086289/0 /scratch/stefan/7769667/working/building/REAL300000086289 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/303 `/scratch/stefan/7769667/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCCC2=NC=C(C(=O)OC)C=C12)C(=O)[O-]) `REAL300000086289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086289 none CCC(NN=C1CCCC2=NC=C(C(=O)OC)C=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 11, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 5, 3, 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 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [35, 22, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 1, 1, 22, 29, 29, 35, 35, 35, 35, 35, 22, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 1] 62 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 35, 39, 29, 30, 31] set([0, 1, 2, 36, 37, 38, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 201 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086289 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086289 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086289/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086289 Building REAL300000086290 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086290' /scratch/stefan/7769667/working/building/REAL300000086290 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086290 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086290/0 /scratch/stefan/7769667/working/building/REAL300000086290 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/304 `/scratch/stefan/7769667/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC(C(C)C)N(C(=O)OC(C)(C)C)C1)C(=O)[O-]) `REAL300000086290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086290 none CCC(NN=C1CC(C(C)C)N(C(=O)OC(C)(C)C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 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: [38, 23, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 7, 7, 20, 25, 25, 25, 1, 23, 34, 34, 38, 38, 38, 38, 38, 23, 7, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1] 107 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 11, 12, 49, 50, 19, 30, 31] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 274 number of broken/clashed sets: 104 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086290 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086290 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086290/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086290 Building REAL300000086291 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086291' /scratch/stefan/7769667/working/building/REAL300000086291 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086291 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086291/0 /scratch/stefan/7769667/working/building/REAL300000086291 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/305 `/scratch/stefan/7769667/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(N2C=C(Cl)C(C)=N2)C=C1)C(=O)[O-]) `REAL300000086291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086291 none CCC(NN=CC1=CC=C(N2C=C(Cl)C(C)=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 16, 1, 5, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 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: [38, 31, 20, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 31, 33, 33, 38, 38, 38, 38, 38, 31, 19, 3, 1, 1, 6, 7, 7, 7, 1, 1] 67 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 17, 18, 37, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086291 none CCC(NN=CC1=CC=C(N2C=C(Cl)C(C)=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 16, 1, 5, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 59, 40, 10, 10, 1, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 59, 59, 59, 67, 67, 67, 67, 67, 59, 39, 10, 6, 6, 1, 2, 2, 2, 6, 6] 67 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 267 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086291 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086291 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086291/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086291 Building REAL300000086292 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086292' /scratch/stefan/7769667/working/building/REAL300000086292 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086292 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086292/0 /scratch/stefan/7769667/working/building/REAL300000086292 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/306 `/scratch/stefan/7769667/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(N2C=CC(C)=N2)C=C1C)C(=O)[O-]) `REAL300000086292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086292 none CCC(NN=CC1=CC=C(N2C=CC(C)=N2)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 8, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [66, 57, 39, 11, 11, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 1, 57, 60, 60, 66, 66, 66, 66, 66, 57, 39, 11, 1, 1, 6, 6, 6, 6, 6, 1, 2, 2, 2] 92 rigid atoms, others: [5, 6, 7, 8, 9, 10, 16, 17, 18, 37, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086292 none CCC(NN=CC1=CC=C(N2C=CC(C)=N2)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 8, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 80, 58, 25, 25, 5, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 80, 83, 83, 92, 92, 92, 92, 92, 80, 58, 25, 6, 6, 1, 1, 2, 2, 2, 6, 6, 6, 6] 92 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 366 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086292 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086292 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086292/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086292 Building REAL300000086293 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086293' /scratch/stefan/7769667/working/building/REAL300000086293 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086293 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086293/0 /scratch/stefan/7769667/working/building/REAL300000086293 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/307 `/scratch/stefan/7769667/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(C(F)(F)C(F)(F)F)C=C1)C(=O)[O-]) `REAL300000086293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086293 none CCC(NN=CC1=CC=C(C(F)(F)C(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 15, 15, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 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: [55, 43, 26, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 43, 52, 52, 55, 55, 55, 55, 55, 43, 25, 5, 1, 1, 1, 1] 91 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086293 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086293 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086293/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086293 Building REAL300000086294 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086294' /scratch/stefan/7769667/working/building/REAL300000086294 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086294 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086294/0 /scratch/stefan/7769667/working/building/REAL300000086294 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/308 `/scratch/stefan/7769667/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(N2C=C(Cl)C=N2)C=C1C)C(=O)[O-]) `REAL300000086294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086294 none CCC(NN=CC1=CC=C(N2C=C(Cl)C=N2)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 16, 1, 8, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 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: [70, 62, 43, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 62, 65, 65, 70, 70, 70, 70, 70, 62, 43, 11, 1, 1, 7, 7, 1, 2, 2, 2] 103 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086294 none CCC(NN=CC1=CC=C(N2C=C(Cl)C=N2)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 16, 1, 8, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 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: [101, 89, 63, 20, 20, 2, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 89, 93, 93, 101, 101, 101, 101, 101, 89, 63, 20, 7, 7, 1, 1, 7, 7, 7, 7] 103 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 399 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086294 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086294 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086294/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086294 Building REAL300000086295 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086295' /scratch/stefan/7769667/working/building/REAL300000086295 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086295 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086295/0 /scratch/stefan/7769667/working/building/REAL300000086295 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/309 `/scratch/stefan/7769667/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1C1=CC=CC=C1Cl)C(=O)[O-]) `REAL300000086295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086295 none CCC(NN=CC1=CC=CC=C1C1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'Cl', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 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, 9, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 5, 9, 9, 9, 13, 13, 13, 13, 13, 9, 8, 5, 1, 1, 1, 1, 5, 5, 3, 5] 15 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086295 none CCC(NN=CC1=CC=CC=C1C1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'Cl', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 13, 9, 9, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 9, 5, 5, 5, 5, 1, 1, 1, 1] 15 rigid atoms, others: [34, 35, 36, 37, 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, 33]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086295 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086295 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086295/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086295 Building REAL300000086296 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086296' /scratch/stefan/7769667/working/building/REAL300000086296 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086296 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086296/0 /scratch/stefan/7769667/working/building/REAL300000086296 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/310 `/scratch/stefan/7769667/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNCC1=C(Br)C=C(CC)S1)C(=O)[O-]) `REAL300000086296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086296 none CCC(=NNCC1=C(Br)C=C(CC)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.3', 'C.3', 'S.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, 5, 1, 8, 8, 5, 1, 1, 17, 1, 1, 5, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens 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, 60, 60, 29, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 60, 78, 78, 122, 122, 122, 122, 122, 29, 5, 5, 1, 8, 8, 9, 9, 9] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 13, 25] set([0, 1, 2, 3, 4, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 535 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086296 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086296 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086296/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086296 Building REAL300000086297 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086297' /scratch/stefan/7769667/working/building/REAL300000086297 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086297 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086297/0 /scratch/stefan/7769667/working/building/REAL300000086297 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/311 `/scratch/stefan/7769667/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC(NC(=O)OC(C)(C)C)C12CCOCC2)C(=O)[O-]) `REAL300000086297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086297 none CCC(NN=C1CC(NC(=O)OC(C)(C)C)C12CCOCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 3, 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, 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: [43, 23, 8, 1, 1, 1, 1, 1, 1, 5, 9, 9, 27, 32, 32, 32, 1, 1, 1, 1, 1, 1, 23, 38, 38, 43, 43, 43, 43, 43, 23, 8, 1, 1, 1, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1] 137 rigid atoms, others: [3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 333 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086297 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086297 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086297/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086297 Building REAL300000086298 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086298' /scratch/stefan/7769667/working/building/REAL300000086298 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086298 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086298/0 /scratch/stefan/7769667/working/building/REAL300000086298 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/312 `/scratch/stefan/7769667/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CSC2=CC=C(C(=O)[O-])C=C12)C(=O)[O-]) `REAL300000086298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086298 none CCC(NN=CC1=CSC2=CC=C(C(=O)[O-])C=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 17, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 19, 19, 22, 22, 22, 22, 22, 17, 13, 4, 1, 1, 1, 1] 22 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086298 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086298 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086298/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086298 Building REAL300000086299 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086299' /scratch/stefan/7769667/working/building/REAL300000086299 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086299 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086299/0 /scratch/stefan/7769667/working/building/REAL300000086299 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/313 `/scratch/stefan/7769667/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC2(CCOC2)OC2=CC=CC=C21)C(=O)[O-]) `REAL300000086299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086299 none CCC(NN=C1CC2(CCOC2)OC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 21, 21, 22, 22, 22, 22, 22, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 22 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086299 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086299 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086299/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086299 Building REAL300000086300 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086300' /scratch/stefan/7769667/working/building/REAL300000086300 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086300 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086300/0 /scratch/stefan/7769667/working/building/REAL300000086300 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/314 `/scratch/stefan/7769667/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(N2CCC(C(=O)OC(C)(C)C)CC2)O1)C(=O)[O-]) `REAL300000086300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086300 none CCC(NN=CC1=CC=C(N2CCC(C(=O)OC(C)(C)C)CC2)O1)C(=O)[O-] 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 16, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 54, 54, 65, 65, 65, 65, 7, 7, 1, 34, 43, 43, 46, 46, 46, 46, 46, 34, 16, 4, 1, 1, 7, 7, 7, 7, 7, 65, 65, 65, 65, 65, 65, 65, 65, 65, 7, 7, 7, 7] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 23] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 366 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086300 none CCC(NN=CC1=CC=C(N2CCC(C(=O)OC(C)(C)C)CC2)O1)C(=O)[O-] 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 71, 49, 19, 19, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 13, 13, 20, 20, 20, 20, 1, 1, 7, 71, 77, 77, 81, 81, 81, 81, 81, 71, 49, 19, 7, 7, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 51, 52, 21, 22, 41, 54, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 369 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086300 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086300 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086300/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086300 Building REAL300000086301 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086301' /scratch/stefan/7769667/working/building/REAL300000086301 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086301 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086301/0 /scratch/stefan/7769667/working/building/REAL300000086301 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/315 `/scratch/stefan/7769667/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=NC=C(Br)C=C1O)C(=O)[O-]) `REAL300000086301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086301 none CCC(NN=CC1=NC=C(Br)C=C1O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [63, 48, 32, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 51, 51, 63, 63, 63, 63, 63, 48, 32, 10, 1, 1, 2] 126 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27]) total number of confs: 260 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086301 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086301/1 /scratch/stefan/7769667/working/building/REAL300000086301 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/316 `/scratch/stefan/7769667/working/3D/316' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=NC=C(Br)C=C1[O-])C(=O)[O-]) `REAL300000086301.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086301 none CCC(NN=CC1=NC=C(Br)C=C1[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 18, 18, 21, 21, 21, 21, 21, 17, 11, 3, 1, 1] 21 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086301 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086301 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086301/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086301/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086301 Building REAL300000086302 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086302' /scratch/stefan/7769667/working/building/REAL300000086302 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086302 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086302/0 /scratch/stefan/7769667/working/building/REAL300000086302 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/317 `/scratch/stefan/7769667/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC2=C(NC(C(=O)OC)=C2)S1)C(=O)[O-]) `REAL300000086302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086302 none CCC(NN=CC1=CC2=C(NC(C(=O)OC)=C2)S1)C(=O)[O-] 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', 'N.pl3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'S.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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 12, 5, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 5, 3, 7, 7, 7, 7, 2, 2, 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: [57, 47, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1, 47, 49, 49, 57, 57, 57, 57, 57, 47, 27, 6, 1, 1, 8, 8, 8, 1] 99 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086302 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086302 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086302/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086302 Building REAL300000086303 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086303' /scratch/stefan/7769667/working/building/REAL300000086303 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086303 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086303/0 /scratch/stefan/7769667/working/building/REAL300000086303 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/318 `/scratch/stefan/7769667/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Cl)=CC(Br)=C1)C(=O)[O-]) `REAL300000086303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086303 none CCC(NN=CC1=CC(Cl)=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [84, 54, 33, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 61, 61, 84, 84, 84, 84, 84, 54, 33, 7, 1, 1, 1] 86 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 392 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086303 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086303 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086303/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086303 Building REAL300000086304 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086304' /scratch/stefan/7769667/working/building/REAL300000086304 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086304 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086304/0 /scratch/stefan/7769667/working/building/REAL300000086304 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/319 `/scratch/stefan/7769667/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1C1=CC=C(C)C=C1C)C(=O)[O-]) `REAL300000086304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086304 none CCC(NN=CC1=CC=CC=C1C1=CC=C(C)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', '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.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 11, 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, 4, 7, 7, 7, 7, 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, 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: [6, 6, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 3, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 11 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, 43]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086304 none CCC(NN=CC1=CC=CC=C1C1=CC=C(C)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', '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.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 11, 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, 4, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 9, 5, 5, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 5, 3, 3, 3, 3, 1, 1, 2, 2, 2, 1, 2, 2, 2] 11 rigid atoms, others: [35, 36, 40, 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, 32, 33, 34, 37, 38, 39, 41, 42, 43]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086304 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086304 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086304/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086304 Building REAL300000086305 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086305' /scratch/stefan/7769667/working/building/REAL300000086305 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086305 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086305/0 /scratch/stefan/7769667/working/building/REAL300000086305 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/320 `/scratch/stefan/7769667/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C(=O)[O-])=CC=C1Br)C(=O)[O-]) `REAL300000086305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086305 none CCC(NN=CC1=CC(C(=O)[O-])=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.co2', 'O.co2', '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, 11, 11, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 47, 33, 11, 11, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 47, 53, 53, 63, 63, 63, 63, 63, 47, 33, 11, 1, 1, 1] 63 rigid atoms, others: [5, 6, 7, 8, 9, 12, 13, 14, 15, 27, 28, 29] set([0, 1, 2, 3, 4, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 280 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086305 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086305 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086305/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086305 Building REAL300000086306 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086306' /scratch/stefan/7769667/working/building/REAL300000086306 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086306 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086306/0 /scratch/stefan/7769667/working/building/REAL300000086306 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/321 `/scratch/stefan/7769667/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(N2CCN(C(=O)OC(C)(C)C)CC2)O1)C(=O)[O-]) `REAL300000086306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086306 none CCC(NN=CC1=CC=C(N2CCN(C(=O)OC(C)(C)C)CC2)O1)C(=O)[O-] 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', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 22, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 52, 57, 57, 57, 13, 13, 1, 42, 60, 60, 66, 66, 66, 66, 66, 42, 21, 6, 1, 1, 13, 13, 13, 13, 57, 57, 57, 57, 57, 57, 57, 57, 57, 13, 13, 13, 13] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 23] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 479 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086306 none CCC(NN=CC1=CC=C(N2CCN(C(=O)OC(C)(C)C)CC2)O1)C(=O)[O-] 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', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 108, 76, 36, 36, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 4, 4, 10, 12, 12, 12, 1, 1, 13, 108, 115, 115, 120, 120, 120, 120, 120, 108, 76, 36, 13, 13, 1, 1, 1, 1, 13, 13, 13, 12, 12, 12, 13, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 50, 51, 52, 21, 22, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 503 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086306 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086306 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086306/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086306 Building REAL300000086307 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086307' /scratch/stefan/7769667/working/building/REAL300000086307 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086307 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086307/0 /scratch/stefan/7769667/working/building/REAL300000086307 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/322 `/scratch/stefan/7769667/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=NC(C2=CC=CC(OC)=C2)=CS1)C(=O)[O-]) `REAL300000086307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086307 none CCC(NN=CC1=NC(C2=CC=CC(OC)=C2)=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'S.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, 5, 5, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 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: [13, 9, 8, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 19, 11, 1, 1, 9, 10, 10, 13, 13, 13, 13, 13, 9, 8, 5, 11, 11, 11, 19, 19, 19, 11, 1] 60 rigid atoms, others: [5, 6, 7, 8, 9, 17, 18, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086307 none CCC(NN=CC1=NC(C2=CC=CC(OC)=C2)=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'S.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, 5, 5, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 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: [41, 40, 36, 27, 27, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 2, 1, 11, 11, 40, 41, 41, 41, 41, 41, 41, 41, 40, 36, 27, 1, 1, 1, 2, 2, 2, 1, 11] 60 rigid atoms, others: [32, 36, 8, 9, 10, 11, 12, 13, 14, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 37]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086307 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086307 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086307/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086307 Building REAL300000086308 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086308' /scratch/stefan/7769667/working/building/REAL300000086308 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086308 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086308/0 /scratch/stefan/7769667/working/building/REAL300000086308 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/323 `/scratch/stefan/7769667/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCCC2=C(OC)C=CC(Cl)=C12)C(=O)[O-]) `REAL300000086308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086308 none CCC(NN=C1CCCC2=C(OC)C=CC(Cl)=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 12, 5, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [30, 19, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 19, 26, 26, 30, 30, 30, 30, 30, 19, 9, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1] 39 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 37, 38] set([0, 1, 2, 35, 36, 12, 34, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 161 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086308 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086308 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086308/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086308 Building REAL300000086309 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086309' /scratch/stefan/7769667/working/building/REAL300000086309 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086309 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086309/0 /scratch/stefan/7769667/working/building/REAL300000086309 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/324 `/scratch/stefan/7769667/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C2=CC=C(F)C=C2)N=C2C=CC(C)=CN21)C(=O)[O-]) `REAL300000086309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086309 none CCC(NN=CC1=C(C2=CC=C(F)C=C2)N=C2C=CC(C)=CN21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.pl3', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 5, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 10, 4, 4, 1, 1, 1, 1, 4, 4, 1, 2, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 13, 15, 15, 16, 16, 16, 16, 16, 13, 10, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1] 16 rigid atoms, others: [43, 5, 6, 7, 8, 39, 15, 16, 17, 18, 19, 20, 21, 22, 38] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086309 none CCC(NN=CC1=C(C2=CC=C(F)C=C2)N=C2C=CC(C)=CN21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.pl3', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 5, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 12, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 16, 16, 16, 16, 16, 16, 16, 14, 12, 7, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4] 16 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086309 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086309 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086309/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086309 Building REAL300000086310 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086310' /scratch/stefan/7769667/working/building/REAL300000086310 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086310 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086310/0 /scratch/stefan/7769667/working/building/REAL300000086310 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/325 `/scratch/stefan/7769667/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC(CC)C(=O)[O-])C1=CC=C(C(F)(F)F)C=C1) `REAL300000086310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086310 none CCC(=NNC(CC)C(=O)[O-])C1=CC=C(C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 5, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 1, 6, 6, 14, 15, 18, 15, 15, 15, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 11, 11, 11, 11, 11, 14, 15, 18, 18, 18, 18, 18, 1, 1, 1, 1] 18 rigid atoms, others: [33, 2, 34, 36, 35, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 89 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086310 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086310 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086310/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086310 Building REAL300000086311 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086311' /scratch/stefan/7769667/working/building/REAL300000086311 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086311 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086311/0 /scratch/stefan/7769667/working/building/REAL300000086311 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/326 `/scratch/stefan/7769667/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(CNC(=O)OC(C)(C)C)C=C1)C(=O)[O-]) `REAL300000086311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086311 none CCC(NN=CC1=CC=C(CNC(=O)OC(C)(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 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, 7, 7, 7] 0 hydrogens 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, 25, 12, 3, 3, 1, 1, 1, 1, 1, 1, 6, 38, 70, 70, 81, 82, 82, 82, 1, 1, 25, 33, 33, 35, 35, 35, 35, 35, 25, 11, 3, 1, 1, 6, 6, 38, 83, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 46, 47, 19, 20] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086311 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086311 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086311/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086311 Building REAL300000086312 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086312' /scratch/stefan/7769667/working/building/REAL300000086312 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086312 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086312/0 /scratch/stefan/7769667/working/building/REAL300000086312 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/327 `/scratch/stefan/7769667/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1CCC(NN=C(CC)C(=O)[O-])CC1C(F)(F)F) `REAL300000086312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086312 none CCOC(=O)C1CCC(NN=C(CC)C(=O)[O-])CC1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', '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, 5, 5, 5, 8, 8, 1, 5, 5, 1, 11, 11, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 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, 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: [8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 6, 7, 7, 19, 7, 15, 15, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 19, 1, 1, 1] 29 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 17, 18, 19, 41, 40, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086312 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086312 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086312/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086312 Building REAL300000086313 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086313' /scratch/stefan/7769667/working/building/REAL300000086313 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086313 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086313/0 /scratch/stefan/7769667/working/building/REAL300000086313 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/328 `/scratch/stefan/7769667/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C(=O)OC)=C2COCCN12)C(=O)[O-]) `REAL300000086313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086313 none CCC(NN=CC1=CC(C(=O)OC)=C2COCCN12)C(=O)[O-] 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', 'O.2', 'O.3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 12, 5, 1, 5, 12, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 5, 3, 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, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 6, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 9, 9, 8, 6, 3, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1] 14 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 39, 13, 14, 15, 16, 17, 18, 38, 30, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086313 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086313 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086313/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086313 Building REAL300000086314 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086314' /scratch/stefan/7769667/working/building/REAL300000086314 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086314 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086314/0 /scratch/stefan/7769667/working/building/REAL300000086314 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/329 `/scratch/stefan/7769667/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(C(=O)N2CCCCC2)C=C1)C(=O)[O-]) `REAL300000086314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086314 none CCC(NN=CC1=CC=C(C(=O)N2CCCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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, 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: [94, 58, 24, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 1, 1, 58, 85, 85, 94, 94, 94, 94, 94, 58, 24, 3, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 161 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 43, 44, 18, 19, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 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: 556 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086314 none CCC(NN=CC1=CC=C(C(=O)N2CCCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [160, 149, 101, 26, 26, 7, 7, 16, 16, 4, 1, 4, 1, 1, 1, 1, 1, 1, 16, 16, 149, 155, 155, 160, 160, 160, 160, 160, 149, 101, 26, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 161 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44]) total number of confs: 632 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086314 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086314 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086314/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086314 Building REAL300000086315 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086315' /scratch/stefan/7769667/working/building/REAL300000086315 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086315 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086315/0 /scratch/stefan/7769667/working/building/REAL300000086315 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/330 `/scratch/stefan/7769667/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC(C(C)C)N(C(=O)OCC2=CC=CC=C2)C1)C(=O)[O-]) `REAL300000086315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086315 none CCC(NN=C1CC(C(C)C)N(C(=O)OCC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 4, 4, 8, 31, 60, 60, 37, 60, 60, 1, 19, 30, 30, 34, 34, 34, 34, 34, 19, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 31, 31, 60, 60, 37, 60, 60, 1, 1] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 11, 12, 50, 35, 22, 51] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 396 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086315 none CCC(NN=C1CC(C(C)C)N(C(=O)OCC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 192, 149, 60, 60, 60, 60, 60, 60, 60, 60, 39, 20, 39, 4, 1, 1, 1, 1, 1, 1, 1, 60, 192, 201, 201, 201, 201, 201, 201, 201, 192, 149, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 4, 4, 1, 1, 1, 1, 1, 60, 60] 201 rigid atoms, others: [48, 49, 45, 46, 15, 16, 17, 18, 19, 20, 21, 47] 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, 38, 39, 40, 41, 42, 43, 44, 50, 51]) total number of confs: 745 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086315 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086315 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086315/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086315 Building REAL300000086316 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086316' /scratch/stefan/7769667/working/building/REAL300000086316 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086316 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086316/0 /scratch/stefan/7769667/working/building/REAL300000086316 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/331 `/scratch/stefan/7769667/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(C(F)(F)F)C(Cl)=C1Cl)C(=O)[O-]) `REAL300000086316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086316 none CCC(NN=CC1=CC=C(C(F)(F)F)C(Cl)=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 16, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 36, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 39, 39, 39, 39, 39, 36, 25, 8, 1, 1] 39 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086316 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086316 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086316/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086316 Building REAL300000086317 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086317' /scratch/stefan/7769667/working/building/REAL300000086317 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086317 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086317/0 /scratch/stefan/7769667/working/building/REAL300000086317 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/332 `/scratch/stefan/7769667/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CNC2=C(C)C(Br)=CC=C12)C(=O)[O-]) `REAL300000086317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086317 none CCC(NN=CC1=CNC2=C(C)C(Br)=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 8, 1, 1, 5, 1, 17, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 59, 38, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 61, 61, 71, 71, 71, 71, 71, 59, 38, 9, 1, 1, 2, 2, 2, 1, 1] 71 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 32, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086317 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086317 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086317/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086317 Building REAL300000086318 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086318' /scratch/stefan/7769667/working/building/REAL300000086318 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086318 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086318/0 /scratch/stefan/7769667/working/building/REAL300000086318 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/333 `/scratch/stefan/7769667/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC(C)C2=CC=C(Br)C=C21)C(=O)[O-]) `REAL300000086318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086318 none CCC(NN=C1CCC(C)C2=CC=C(Br)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 22, 22, 24, 24, 24, 24, 24, 19, 8, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1] 24 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 35, 36, 37] set([0, 1, 2, 33, 32, 34, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 113 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086318 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086318 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086318/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086318 Building REAL300000086319 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086319' /scratch/stefan/7769667/working/building/REAL300000086319 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086319 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086319/0 /scratch/stefan/7769667/working/building/REAL300000086319 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/334 `/scratch/stefan/7769667/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCOC2=C1C=CC(Br)=C2F)C(=O)[O-]) `REAL300000086319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086319 none CCC(NN=C1CCOC2=C1C=CC(Br)=C2F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 12, 1, 1, 1, 1, 1, 17, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 23, 23, 23, 23, 23, 23, 23, 20, 8, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31] set([0, 1, 2, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 104 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086319 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086319 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086319/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086319 Building REAL300000086320 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086320' /scratch/stefan/7769667/working/building/REAL300000086320 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086320 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086320/0 /scratch/stefan/7769667/working/building/REAL300000086320 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/335 `/scratch/stefan/7769667/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(S(N)(=O)=O)C=C1Br)C(=O)[O-]) `REAL300000086320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086320 none CCC(NN=CC1=CC=C(S(N)(=O)=O)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', '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, 14, 8, 11, 11, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 2, 2, 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: [57, 49, 31, 9, 9, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 49, 49, 49, 57, 57, 57, 57, 57, 49, 31, 9, 1, 1, 5, 5, 1] 146 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 238 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086320 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086320 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086320/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086320 Building REAL300000086321 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086321' /scratch/stefan/7769667/working/building/REAL300000086321 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086321 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086321/0 /scratch/stefan/7769667/working/building/REAL300000086321 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/336 `/scratch/stefan/7769667/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(Cl)C=CC=C1Br)C(=O)[O-]) `REAL300000086321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086321 none CCC(NN=CC1=C(Cl)C=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 59, 37, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 60, 60, 77, 77, 77, 77, 77, 59, 37, 10, 1, 1, 1] 77 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 310 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086321 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086321 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086321/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086321 Building REAL300000086322 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086322' /scratch/stefan/7769667/working/building/REAL300000086322 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086322 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086322/0 /scratch/stefan/7769667/working/building/REAL300000086322 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/337 `/scratch/stefan/7769667/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(F)C(Br)=C1F)C(=O)[O-]) `REAL300000086322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086322 none CCC(NN=CC1=CC=C(F)C(Br)=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 17, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 40, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 41, 41, 51, 51, 51, 51, 51, 40, 29, 10, 1, 1] 51 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086322 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086322 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086322/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086322 Building REAL300000086323 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086323' /scratch/stefan/7769667/working/building/REAL300000086323 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086323 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086323/0 /scratch/stefan/7769667/working/building/REAL300000086323 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/338 `/scratch/stefan/7769667/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC(C)(C)C1=C(F)C=CC=C1Br)C(=O)[O-]) `REAL300000086323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086323 none CCC(NN=CC(C)(C)C1=C(F)C=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', '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, 5, 5, 1, 1, 15, 1, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 12, 12, 8, 8, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 17, 17, 17, 17, 17, 12, 12, 8, 3, 3, 3, 3, 3, 3, 1, 1, 1] 17 rigid atoms, others: [34, 35, 36, 6, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086323 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086323 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086323/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086323 Building REAL300000086324 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086324' /scratch/stefan/7769667/working/building/REAL300000086324 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086324 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086324/0 /scratch/stefan/7769667/working/building/REAL300000086324 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/339 `/scratch/stefan/7769667/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=NC=C(Br)C=C1C)C(=O)[O-]) `REAL300000086324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086324 none CCC(NN=CC1=NC=C(Br)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [82, 59, 40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 64, 64, 82, 82, 82, 82, 82, 59, 40, 9, 1, 1, 2, 2, 2] 86 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 357 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086324 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086324 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086324/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086324 Building REAL300000086325 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086325' /scratch/stefan/7769667/working/building/REAL300000086325 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086325 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086325/0 /scratch/stefan/7769667/working/building/REAL300000086325 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/340 `/scratch/stefan/7769667/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCN(C(=O)OC(C)(C)C)CC1(C)C)C(=O)[O-]) `REAL300000086325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086325 none CCC(NN=C1CCN(C(=O)OC(C)(C)C)CC1(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 3, 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, 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: [47, 28, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 21, 21, 21, 1, 1, 1, 1, 28, 42, 42, 47, 47, 47, 47, 47, 28, 8, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 2, 2, 2, 2, 2, 2] 104 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 43, 44, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50]) total number of confs: 324 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086325 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086325 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086325/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086325 Building REAL300000086326 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086326' /scratch/stefan/7769667/working/building/REAL300000086326 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086326 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086326/0 /scratch/stefan/7769667/working/building/REAL300000086326 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/341 `/scratch/stefan/7769667/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC(CC)N(C(=O)OC(C)(C)C)C1)C(=O)[O-]) `REAL300000086326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086326 none CCC(NN=C1CC(CC)N(C(=O)OC(C)(C)C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 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: [42, 24, 7, 1, 1, 1, 1, 1, 1, 3, 1, 1, 7, 7, 23, 27, 27, 27, 1, 24, 38, 38, 42, 42, 42, 42, 42, 24, 7, 1, 1, 1, 3, 3, 3, 3, 3, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1] 141 rigid atoms, others: [3, 4, 5, 6, 7, 8, 10, 11, 46, 47, 18, 29, 30, 31] set([0, 1, 2, 9, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 307 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086326 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086326 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086326/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086326 Building REAL300000086327 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086327' /scratch/stefan/7769667/working/building/REAL300000086327 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086327 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086327/0 /scratch/stefan/7769667/working/building/REAL300000086327 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/342 `/scratch/stefan/7769667/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(S(=O)(=O)C(F)F)=C1)C(=O)[O-]) `REAL300000086327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086327 none CCC(NN=CC1=CC=CC(S(=O)(=O)C(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 14, 11, 11, 5, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 80, 39, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 19, 19, 1, 80, 104, 104, 117, 117, 117, 117, 117, 80, 38, 9, 1, 1, 1, 19, 1] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 11, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 651 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086327 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086327 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086327/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086327 Building REAL300000086328 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086328' /scratch/stefan/7769667/working/building/REAL300000086328 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086328 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086328/0 /scratch/stefan/7769667/working/building/REAL300000086328 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/343 `/scratch/stefan/7769667/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC(C2CCOCC2)=NN1C)C(=O)[O-]) `REAL300000086328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086328 none CCC(NN=C(C)C1=CC(C2CCOCC2)=NN1C)C(=O)[O-] 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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 8, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [34, 24, 16, 5, 5, 1, 5, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 24, 26, 26, 34, 34, 34, 34, 34, 24, 16, 5, 5, 5, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2] 68 rigid atoms, others: [32, 5, 7, 8, 9, 10, 16, 17, 18] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086328 none CCC(NN=C(C)C1=CC(C2CCOCC2)=NN1C)C(=O)[O-] 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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 8, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 63, 58, 30, 30, 13, 30, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 63, 68, 68, 68, 68, 68, 68, 68, 63, 58, 30, 30, 30, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13] 68 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 231 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086328 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086328 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086328/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086328 Building REAL300000086329 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086329' /scratch/stefan/7769667/working/building/REAL300000086329 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086329 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086329/0 /scratch/stefan/7769667/working/building/REAL300000086329 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/344 `/scratch/stefan/7769667/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C2CCN(C(=O)OCC3=CC=CC=C3)C2=C1)C(=O)[O-]) `REAL300000086329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086329 none CCC(NN=CC1=CC=C2CCN(C(=O)OCC3=CC=CC=C3)C2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', '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', '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, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 7] 0 hydrogens 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, 38, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 28, 49, 49, 31, 49, 49, 1, 1, 38, 50, 50, 51, 51, 51, 51, 51, 38, 19, 6, 1, 1, 1, 1, 1, 1, 27, 27, 49, 49, 49, 49, 49, 1] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23, 24, 39, 49, 38, 37] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 469 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086329 none CCC(NN=CC1=CC=C2CCN(C(=O)OCC3=CC=CC=C3)C2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', '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', '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, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 151, 113, 113, 49, 49, 49, 48, 48, 48, 48, 26, 18, 26, 3, 1, 1, 1, 1, 1, 1, 1, 48, 49, 196, 201, 201, 201, 201, 201, 201, 201, 196, 151, 113, 49, 48, 48, 48, 48, 48, 3, 3, 1, 1, 1, 1, 1, 49] 201 rigid atoms, others: [48, 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, 39, 40, 41, 42, 43, 49]) total number of confs: 731 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086329 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086329 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086329/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086329 Building REAL300000086330 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086330' /scratch/stefan/7769667/working/building/REAL300000086330 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086330 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086330/0 /scratch/stefan/7769667/working/building/REAL300000086330 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/345 `/scratch/stefan/7769667/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=NC(Br)=C1F)C(=O)[O-]) `REAL300000086330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086330 none CCC(NN=CC1=CC=NC(Br)=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 1, 17, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 40, 40, 50, 50, 50, 50, 50, 39, 27, 9, 1, 1] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086330 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086330 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086330/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086330 Building REAL300000086331 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086331' /scratch/stefan/7769667/working/building/REAL300000086331 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086331 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086331/0 /scratch/stefan/7769667/working/building/REAL300000086331 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/346 `/scratch/stefan/7769667/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C(=O)[O-])=CC(Br)=C1O)C(=O)[O-]) `REAL300000086331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086331 none CCC(NN=CC1=CC(C(=O)[O-])=CC(Br)=C1O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 11, 11, 1, 1, 17, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [53, 44, 32, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 47, 47, 53, 53, 53, 53, 53, 44, 32, 12, 1, 1, 2] 106 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 213 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086331 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086331/1 /scratch/stefan/7769667/working/building/REAL300000086331 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/347 `/scratch/stefan/7769667/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C(=O)[O-])=CC(Br)=C1[O-])C(=O)[O-]) `REAL300000086331.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086331 none CCC(NN=CC1=CC(C(=O)[O-])=CC(Br)=C1[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 20, 20, 23, 23, 23, 23, 23, 19, 15, 4, 1, 1] 23 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086331 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086331 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086331/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086331/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086331 Building REAL300000086332 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086332' /scratch/stefan/7769667/working/building/REAL300000086332 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086332 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086332/0 /scratch/stefan/7769667/working/building/REAL300000086332 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/348 `/scratch/stefan/7769667/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=C(C)N=C1Cl)C(=O)[O-]) `REAL300000086332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086332 none CCC(NN=CC1=CC(Br)=C(C)N=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 5, 8, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 36, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 47, 47, 47, 47, 47, 36, 26, 8, 1, 2, 2, 2] 47 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086332 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086332 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086332/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086332 Building REAL300000086333 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086333' /scratch/stefan/7769667/working/building/REAL300000086333 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086333 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086333/0 /scratch/stefan/7769667/working/building/REAL300000086333 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/349 `/scratch/stefan/7769667/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCCN(C(=O)OCC2=CC=CC=C2)C2=CC=CC=C21)C(=O)[O-]) `REAL300000086333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086333 none CCC(NN=C1CCCN(C(=O)OCC2=CC=CC=C2)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', '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.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 56, 99, 99, 61, 99, 99, 1, 1, 1, 1, 1, 1, 16, 28, 28, 31, 31, 31, 31, 31, 16, 5, 1, 1, 1, 1, 1, 1, 56, 56, 99, 99, 99, 99, 99, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 49, 50, 51, 52] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 585 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086333 none CCC(NN=C1CCCN(C(=O)OCC2=CC=CC=C2)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', '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.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 161, 99, 99, 99, 99, 99, 99, 60, 24, 60, 3, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 99, 99, 183, 201, 201, 201, 201, 201, 201, 201, 183, 161, 99, 99, 99, 99, 99, 99, 3, 3, 1, 1, 1, 1, 1, 99, 99, 99, 99] 201 rigid atoms, others: [48, 45, 44, 13, 14, 15, 16, 17, 18, 19, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 49, 50, 51, 52]) total number of confs: 723 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086333 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086333 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086333/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086333 Building REAL300000086334 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086334' /scratch/stefan/7769667/working/building/REAL300000086334 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086334 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086334/0 /scratch/stefan/7769667/working/building/REAL300000086334 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/350 `/scratch/stefan/7769667/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=CC(OC)=C1OCC(=O)[O-])C(=O)[O-]) `REAL300000086334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086334 none CCC(NN=CC1=CC(Br)=CC(OC)=C1OCC(=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 12, 5, 1, 12, 5, 1, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 2, 2, 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: [35, 18, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 3, 13, 25, 25, 18, 28, 28, 35, 35, 35, 35, 35, 18, 6, 4, 1, 1, 4, 4, 4, 13, 13] 101 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 31] set([0, 1, 2, 3, 4, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 275 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086334 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086334 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086334/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086334 Building REAL300000086335 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086335' /scratch/stefan/7769667/working/building/REAL300000086335 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086335 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086335/0 /scratch/stefan/7769667/working/building/REAL300000086335 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/351 `/scratch/stefan/7769667/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1)C(=O)[O-]) `REAL300000086335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086335 none CCC(NN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 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: [80, 48, 28, 6, 6, 1, 1, 1, 1, 1, 1, 2, 7, 35, 35, 35, 35, 35, 35, 35, 1, 1, 48, 72, 72, 80, 80, 80, 80, 80, 48, 28, 6, 1, 1, 7, 7, 35, 35, 1, 1] 201 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 39, 40, 20, 21] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 488 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086335 none CCC(NN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 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: [201, 194, 145, 75, 75, 35, 35, 35, 35, 19, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 194, 201, 201, 201, 201, 201, 201, 201, 194, 145, 75, 35, 35, 9, 9, 1, 1, 35, 35] 201 rigid atoms, others: [37, 38, 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, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 757 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086335 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086335 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086335/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086335 Building REAL300000086336 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086336' /scratch/stefan/7769667/working/building/REAL300000086336 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086336 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086336/0 /scratch/stefan/7769667/working/building/REAL300000086336 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/352 `/scratch/stefan/7769667/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(I)=CC(C(=O)[O-])=C1)C(=O)[O-]) `REAL300000086336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086336 none CCC(NN=CC1=CC(I)=CC(C(=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 26, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 33, 33, 33, 33, 33, 26, 19, 7, 1, 1, 1] 33 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086336 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086336 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086336/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086336 Building REAL300000086337 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086337' /scratch/stefan/7769667/working/building/REAL300000086337 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086337 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086337/0 /scratch/stefan/7769667/working/building/REAL300000086337 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/353 `/scratch/stefan/7769667/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C(=O)NC2=CC=C(I)C=C21)C(=O)[O-]) `REAL300000086337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086337 none CCC(NN=C1C(=O)NC2=CC=C(I)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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, 5, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 16, 16, 21, 21, 21, 21, 21, 15, 5, 1, 1, 1, 1] 21 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29] set([0, 1, 2, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086337 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086337 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086337/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086337 Building REAL300000086338 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086338' /scratch/stefan/7769667/working/building/REAL300000086338 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086338 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086338/0 /scratch/stefan/7769667/working/building/REAL300000086338 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/354 `/scratch/stefan/7769667/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1COC2=C(Br)C=CC=C12)C(=O)[O-]) `REAL300000086338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086338 none CCC(NN=C1COC2=C(Br)C=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 17, 17, 22, 22, 22, 22, 22, 16, 7, 1, 1, 1, 1, 1] 22 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086338 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086338 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086338/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086338 Building REAL300000086339 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086339' /scratch/stefan/7769667/working/building/REAL300000086339 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086339 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086339/0 /scratch/stefan/7769667/working/building/REAL300000086339 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/355 `/scratch/stefan/7769667/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(Br)=CC(F)=C1CNN=C(CC)C(=O)[O-]) `REAL300000086339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086339 none CCOC1=CC(Br)=CC(F)=C1CNN=C(CC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 1, 15, 1, 5, 8, 8, 1, 5, 5, 1, 11, 11, 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, 4, 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 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 26, 63, 63, 156, 63, 97, 97, 18, 18, 18, 17, 17, 1, 1, 6, 6, 26, 156, 156, 156, 156, 156] 181 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26] set([0, 1, 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: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086339 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086339 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086339/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086339 Building REAL300000086340 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086340' /scratch/stefan/7769667/working/building/REAL300000086340 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086340 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086340/0 /scratch/stefan/7769667/working/building/REAL300000086340 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/356 `/scratch/stefan/7769667/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(I)N=CN1C)C(=O)[O-]) `REAL300000086340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086340 none CCC(NN=CC1=C(I)N=CN1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'I', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 18, 8, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 36, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 36, 37, 37, 48, 48, 48, 48, 48, 36, 25, 5, 1, 2, 2, 2] 48 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 24] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086340 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086340 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086340/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086340 Building REAL300000086341 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086341' /scratch/stefan/7769667/working/building/REAL300000086341 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086341 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086341/0 /scratch/stefan/7769667/working/building/REAL300000086341 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/357 `/scratch/stefan/7769667/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(O)C(C(=O)[O-])=CC2=CC=CC=C21)C(=O)[O-]) `REAL300000086341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086341 none CCC(NN=CC1=C(O)C(C(=O)[O-])=CC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [35, 30, 23, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 30, 34, 34, 35, 35, 35, 35, 35, 30, 23, 9, 2, 1, 1, 1, 1, 1] 70 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086341 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086341 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086341/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086341 Building REAL300000086342 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086342' /scratch/stefan/7769667/working/building/REAL300000086342 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086342 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086342/0 /scratch/stefan/7769667/working/building/REAL300000086342 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/358 `/scratch/stefan/7769667/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C(=O)NC2=CC=C(OCCF)C=C21)C(=O)[O-]) `REAL300000086342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086342 none CCC(NN=C1C(=O)NC2=CC=C(OCCF)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 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 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [47, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 39, 1, 1, 28, 41, 41, 47, 47, 47, 47, 47, 28, 6, 1, 1, 1, 22, 22, 39, 39, 1] 178 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 36, 29, 30, 31] set([0, 1, 2, 35, 33, 32, 34, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 401 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086342 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086342 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086342/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086342 Building REAL300000086343 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086343' /scratch/stefan/7769667/working/building/REAL300000086343 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300000086343 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086343/0 /scratch/stefan/7769667/working/building/REAL300000086343 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/359 `/scratch/stefan/7769667/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC(C)N(CC2=CC=CC=C2)C1)C(=O)[O-]) `REAL300000086343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086343 none CCC(NN=C1CCC(C)N(CC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 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, 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: [30, 17, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 17, 24, 24, 30, 30, 30, 30, 30, 17, 8, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 8, 8, 8, 8, 8, 1, 1] 51 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 44, 45, 18, 29, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 190 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086343 none CCC(NN=C1CCC(C)N(CC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 42, 26, 8, 8, 8, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 8, 42, 46, 46, 51, 51, 51, 51, 51, 42, 26, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 8, 8] 51 rigid atoms, others: [43, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45]) total number of confs: 222 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086343 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086343/1 /scratch/stefan/7769667/working/building/REAL300000086343 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/360 `/scratch/stefan/7769667/working/3D/360' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC(C)[N@H+](CC2=CC=CC=C2)C1)C(=O)[O-]) `REAL300000086343.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086343/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086343 none CCC(NN=C1CCC(C)[N@H+](CC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 1, 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, 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, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 1, 16, 20, 20, 21, 21, 21, 21, 21, 16, 7, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 5, 5, 5, 5, 5, 1, 1] 29 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 45, 46, 19, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 117 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086343 none CCC(NN=C1CCC(C)[N@H+](CC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 1, 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, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 26, 13, 5, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 5, 26, 29, 29, 29, 29, 29, 29, 29, 26, 13, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 1, 1, 1, 1, 5, 5] 29 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 44] 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, 35, 36, 37, 38, 39, 45, 46]) total number of confs: 127 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086343 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `2' /scratch/stefan/7769667/working/building/REAL300000086343/2 /scratch/stefan/7769667/working/building/REAL300000086343 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 2 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/361 `/scratch/stefan/7769667/working/3D/361' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC(C)[N@@H+](CC2=CC=CC=C2)C1)C(=O)[O-]) `REAL300000086343.mol2' -> `2.mol2' `temp.mol2' -> `REAL300000086343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086343/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086343 none CCC(NN=C1CCC(C)[N@@H+](CC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 1, 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, 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, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 4, 5, 5, 1, 16, 20, 20, 21, 21, 21, 21, 21, 16, 7, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 5, 5, 5, 5, 5, 1, 1] 29 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 45, 46, 19, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 122 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086343 none CCC(NN=C1CCC(C)[N@@H+](CC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 1, 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, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 26, 13, 5, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 5, 26, 29, 29, 29, 29, 29, 29, 29, 26, 13, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 1, 1, 1, 1, 5, 5] 29 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 44] 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, 35, 36, 37, 38, 39, 45, 46]) total number of confs: 127 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086343 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086343 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 2: /scratch/stefan/7769667/working/building/REAL300000086343/2.* 0: /scratch/stefan/7769667/working/building/REAL300000086343/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086343/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086343 Building REAL300000086344 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086344' /scratch/stefan/7769667/working/building/REAL300000086344 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086344 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086344/0 /scratch/stefan/7769667/working/building/REAL300000086344 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/362 `/scratch/stefan/7769667/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC(C)(C2=CC=CC(Br)=C2)CC1)C(=O)[O-]) `REAL300000086344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086344 none CCC(NN=C1CCC(C)(C2=CC=CC(Br)=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 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: [29, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 13, 13, 1, 1, 17, 25, 25, 29, 29, 29, 29, 29, 17, 6, 1, 1, 1, 1, 2, 2, 2, 13, 13, 12, 13, 1, 1, 1, 1] 139 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 43, 17, 18, 42, 41, 40, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 184 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086344 none CCC(NN=C1CCC(C)(C2=CC=CC(Br)=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 113, 54, 13, 13, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 113, 133, 133, 140, 140, 140, 140, 140, 113, 54, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13] 140 rigid atoms, others: [36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 660 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086344 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086344 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086344/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086344 Building REAL300000086345 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086345' /scratch/stefan/7769667/working/building/REAL300000086345 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086345 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086345/0 /scratch/stefan/7769667/working/building/REAL300000086345 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/363 `/scratch/stefan/7769667/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1)C(=O)[O-]) `REAL300000086345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086345 none CCC(NN=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [60, 45, 24, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 24, 24, 5, 1, 1, 45, 55, 55, 60, 60, 60, 60, 60, 45, 23, 5, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1] 173 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 20, 21, 41, 42] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086345 none CCC(NN=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [124, 105, 65, 19, 13, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 5, 5, 105, 115, 115, 124, 124, 124, 124, 124, 105, 65, 13, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5] 173 rigid atoms, others: [35, 36, 40, 9, 10, 11, 12, 13, 14, 15, 19, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 41, 42]) total number of confs: 537 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086345 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086345 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086345/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086345 Building REAL300000086346 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086346' /scratch/stefan/7769667/working/building/REAL300000086346 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086346 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086346/0 /scratch/stefan/7769667/working/building/REAL300000086346 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/364 `/scratch/stefan/7769667/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(CNN=C(CC)C(=O)[O-])=CC=C1OCC(=O)[O-]) `REAL300000086346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086346 none CCOC1=CC(CNN=C(CC)C(=O)[O-])=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 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: [4, 4, 1, 1, 1, 1, 1, 2, 6, 6, 6, 29, 6, 13, 13, 1, 1, 1, 1, 9, 33, 50, 50, 4, 4, 4, 4, 4, 1, 2, 2, 6, 29, 29, 29, 29, 29, 1, 1, 33, 33] 91 rigid atoms, others: [2, 3, 4, 5, 6, 15, 16, 17, 18, 38, 28, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086346 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086346 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086346/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086346 Building REAL300000086347 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086347' /scratch/stefan/7769667/working/building/REAL300000086347 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086347 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086347/0 /scratch/stefan/7769667/working/building/REAL300000086347 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/365 `/scratch/stefan/7769667/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(OCC2=CC=C(C(=O)OC)O2)C=C1)C(=O)[O-]) `REAL300000086347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086347 none CCC(NN=CC1=CC=C(OCC2=CC=C(C(=O)OC)O2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 12, 5, 1, 1, 1, 1, 1, 11, 12, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 5, 3, 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: [32, 22, 11, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 17, 17, 17, 17, 49, 49, 49, 17, 1, 1, 22, 31, 31, 32, 32, 32, 32, 32, 22, 11, 4, 1, 1, 2, 2, 17, 17, 49, 49, 49, 1, 1] 201 rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 43, 44, 21, 22] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086347 none CCC(NN=CC1=CC=C(OCC2=CC=C(C(=O)OC)O2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 12, 5, 1, 1, 1, 1, 1, 11, 12, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 5, 3, 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: [172, 148, 91, 44, 44, 17, 17, 17, 17, 9, 9, 1, 1, 1, 1, 1, 1, 6, 6, 6, 1, 17, 17, 148, 169, 169, 172, 172, 172, 172, 172, 148, 91, 44, 17, 17, 9, 9, 1, 1, 6, 6, 6, 17, 17] 201 rigid atoms, others: [38, 39, 11, 12, 13, 14, 15, 16, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 779 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086347 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086347 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086347/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086347 Building REAL300000086348 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086348' /scratch/stefan/7769667/working/building/REAL300000086348 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086348 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086348/0 /scratch/stefan/7769667/working/building/REAL300000086348 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/366 `/scratch/stefan/7769667/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC2=C(C=C1)N(CC1=CC=CC=C1)C1=C2C=CC=C1)C(=O)[O-]) `REAL300000086348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086348 none CCC(NN=CC1=CC2=C(C=C1)N(CC1=CC=CC=C1)C1=C2C=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 59, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 12, 12, 7, 12, 12, 1, 1, 1, 1, 1, 1, 59, 62, 62, 65, 65, 65, 65, 65, 59, 33, 9, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 37, 38, 39, 47, 48, 49, 50] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086348 none CCC(NN=CC1=CC2=C(C=C1)N(CC1=CC=CC=C1)C1=C2C=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 139, 75, 75, 12, 12, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 199, 201, 201, 201, 201, 201, 201, 201, 199, 139, 75, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 12, 12, 12, 12] 201 rigid atoms, others: [45, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50]) total number of confs: 736 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086348 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086348 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086348/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086348 Building REAL300000086349 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086349' /scratch/stefan/7769667/working/building/REAL300000086349 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086349 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086349/0 /scratch/stefan/7769667/working/building/REAL300000086349 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/367 `/scratch/stefan/7769667/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C)SC(C)=C1Br)C(=O)[O-]) `REAL300000086349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086349 none CCC(NN=CC1=C(C)SC(C)=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'Br', '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, 5, 5, 8, 8, 1, 1, 1, 5, 14, 1, 5, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 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: [78, 62, 48, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 71, 71, 78, 78, 78, 78, 78, 62, 48, 12, 2, 2, 2, 2, 2, 2] 83 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 338 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086349 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086349 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086349/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086349 Building REAL300000086350 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086350' /scratch/stefan/7769667/working/building/REAL300000086350 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086350 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086350/0 /scratch/stefan/7769667/working/building/REAL300000086350 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/368 `/scratch/stefan/7769667/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(C)N=C1C1=CC=CC(F)=C1)C(=O)[O-]) `REAL300000086350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086350 none CCC(NN=CC1=CN(C)N=C1C1=CC=CC(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'F', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 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: [79, 54, 29, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 9, 11, 11, 11, 54, 67, 67, 79, 79, 79, 79, 79, 54, 29, 11, 1, 2, 2, 2, 11, 11, 11, 11] 159 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 410 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086350 none CCC(NN=CC1=CN(C)N=C1C1=CC=CC(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'F', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [159, 139, 102, 47, 47, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 139, 158, 158, 159, 159, 159, 159, 159, 139, 102, 47, 11, 11, 11, 11, 1, 1, 1, 1] 159 rigid atoms, others: [34, 35, 36, 37, 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, 33]) total number of confs: 666 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086350 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086350 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086350/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086350 Building REAL300000086351 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086351' /scratch/stefan/7769667/working/building/REAL300000086351 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086351 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086351/0 /scratch/stefan/7769667/working/building/REAL300000086351 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/369 `/scratch/stefan/7769667/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC(C2=CC=CC=C2Br)C1)C(=O)[O-]) `REAL300000086351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086351 none CCC(NN=C1CC(C2=CC=CC=C2Br)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 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: [38, 23, 8, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 6, 1, 23, 33, 33, 38, 38, 38, 38, 38, 23, 8, 1, 1, 1, 6, 6, 1, 6, 1, 1] 74 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 15, 26, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32]) total number of confs: 214 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086351 none CCC(NN=C1CC(C2=CC=CC=C2Br)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 59, 33, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 59, 65, 65, 74, 74, 74, 74, 74, 59, 33, 6, 6, 6, 1, 1, 1, 1, 6, 6] 74 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 323 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086351 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086351 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086351/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086351 Building REAL300000086352 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086352' /scratch/stefan/7769667/working/building/REAL300000086352 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086352 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086352/0 /scratch/stefan/7769667/working/building/REAL300000086352 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/370 `/scratch/stefan/7769667/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCCC2=CC=C(Br)C=C2C1)C(=O)[O-]) `REAL300000086352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086352 none CCC(NN=C1CCCC2=CC=C(Br)C=C2C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 15, 15, 19, 19, 19, 19, 19, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 19 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 86 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086352 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086352 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086352/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086352 Building REAL300000086353 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086353' /scratch/stefan/7769667/working/building/REAL300000086353 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086353 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086353/0 /scratch/stefan/7769667/working/building/REAL300000086353 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/371 `/scratch/stefan/7769667/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(OC(F)(F)F)C=C1F)C(=O)[O-]) `REAL300000086353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086353 none CCC(NN=CC1=CC=C(OC(F)(F)F)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 12, 5, 15, 15, 15, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 54, 29, 7, 7, 1, 1, 1, 1, 1, 1, 13, 31, 31, 31, 1, 1, 1, 54, 75, 75, 83, 83, 83, 83, 83, 54, 28, 7, 1, 1, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 517 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086353 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086353 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086353/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086353 Building REAL300000086354 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086354' /scratch/stefan/7769667/working/building/REAL300000086354 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086354 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086354/0 /scratch/stefan/7769667/working/building/REAL300000086354 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/372 `/scratch/stefan/7769667/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(C(F)(F)C(F)(F)F)=C1)C(=O)[O-]) `REAL300000086354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086354 none CCC(NN=CC1=CC=CC(C(F)(F)C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 15, 15, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 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, 10, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 10, 10, 10, 13, 13, 13, 13, 13, 10, 8, 6, 1, 1, 1, 1] 26 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 18, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086354 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086354 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086354/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086354 Building REAL300000086355 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086355' /scratch/stefan/7769667/working/building/REAL300000086355 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086355 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086355/0 /scratch/stefan/7769667/working/building/REAL300000086355 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/373 `/scratch/stefan/7769667/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(N2C=CN=C2C)C=C1C)C(=O)[O-]) `REAL300000086355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086355 none CCC(NN=CC1=CC=C(N2C=CN=C2C)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 56, 39, 12, 12, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 1, 56, 59, 59, 62, 62, 62, 62, 62, 56, 39, 12, 1, 1, 10, 10, 10, 10, 10, 1, 2, 2, 2] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 16, 17, 18, 37, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 248 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086355 none CCC(NN=CC1=CC=C(N2C=CN=C2C)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7] 0 hydrogens 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, 163, 102, 23, 25, 1, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 154, 172, 170, 188, 187, 184, 186, 186, 164, 102, 25, 10, 10, 1, 1, 2, 2, 2, 10, 10, 10, 10] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 828 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086355 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086355 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086355/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086355 Building REAL300000086356 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086356' /scratch/stefan/7769667/working/building/REAL300000086356 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086356 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086356/0 /scratch/stefan/7769667/working/building/REAL300000086356 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/374 `/scratch/stefan/7769667/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(N2C=NC(C)=C2C)C=C1)C(=O)[O-]) `REAL300000086356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086356 none CCC(NN=CC1=CC=C(N2C=NC(C)=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 8, 1, 5, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 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: [62, 48, 26, 5, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1, 48, 57, 57, 62, 62, 62, 62, 62, 48, 25, 5, 1, 1, 10, 10, 10, 10, 10, 10, 10, 1, 1] 135 rigid atoms, others: [5, 6, 7, 8, 9, 10, 39, 17, 18, 40, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 289 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086356 none CCC(NN=CC1=CC=C(N2C=NC(C)=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 8, 1, 5, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [135, 115, 80, 20, 13, 1, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 115, 122, 122, 135, 135, 135, 135, 135, 115, 80, 13, 10, 10, 1, 2, 2, 2, 2, 2, 2, 10, 10] 135 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 555 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086356 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086356 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086356/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086356 Building REAL300000086357 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086357' /scratch/stefan/7769667/working/building/REAL300000086357 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086357 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086357/0 /scratch/stefan/7769667/working/building/REAL300000086357 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/375 `/scratch/stefan/7769667/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(C2CCOCC2)N=C1C(=O)[O-])C(=O)[O-]) `REAL300000086357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086357 none CCC(NN=CC1=CN(C2CCOCC2)N=C1C(=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 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 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [33, 20, 11, 4, 4, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 2, 2, 20, 26, 26, 33, 33, 33, 33, 33, 20, 11, 4, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13] 92 rigid atoms, others: [5, 6, 7, 8, 9, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 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: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086357 none CCC(NN=CC1=CN(C2CCOCC2)N=C1C(=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 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 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 75, 52, 19, 19, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 22, 22, 75, 90, 90, 92, 92, 92, 92, 92, 75, 52, 19, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 92 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 442 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086357 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086357 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086357/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086357 Building REAL300000086358 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086358' /scratch/stefan/7769667/working/building/REAL300000086358 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086358 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086358/0 /scratch/stefan/7769667/working/building/REAL300000086358 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/376 `/scratch/stefan/7769667/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C(=O)[O-])N(C)C2=CC=C(F)C=C21)C(=O)[O-]) `REAL300000086358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086358 none CCC(NN=CC1=C(C(=O)[O-])N(C)C2=CC=C(F)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 8, 8, 1, 1, 1, 1, 11, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 22, 15, 4, 4, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 26, 26, 29, 29, 29, 29, 29, 22, 15, 4, 2, 2, 2, 1, 1, 1] 29 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 33, 32, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086358 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086358 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086358/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086358 Building REAL300000086359 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086359' /scratch/stefan/7769667/working/building/REAL300000086359 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086359 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086359/0 /scratch/stefan/7769667/working/building/REAL300000086359 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/377 `/scratch/stefan/7769667/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C(=O)NC2=C(OC)C=CC(Br)=C12)C(=O)[O-]) `REAL300000086359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086359 none CCC(NN=C1C(=O)NC2=C(OC)C=CC(Br)=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 1, 1, 12, 5, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 3, 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 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [29, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 20, 27, 27, 29, 29, 29, 29, 29, 20, 7, 1, 4, 4, 4, 1, 1] 32 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086359 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086359 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086359/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086359 Building REAL300000086360 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086360' /scratch/stefan/7769667/working/building/REAL300000086360 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086360 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086360/0 /scratch/stefan/7769667/working/building/REAL300000086360 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/378 `/scratch/stefan/7769667/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC2=C(Br)C=CC=C2S1)C(=O)[O-]) `REAL300000086360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086360 none CCC(NN=CC1=CC2=C(Br)C=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 49, 32, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 53, 53, 68, 68, 68, 68, 68, 49, 32, 6, 1, 1, 1, 1] 68 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086360 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086360 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086360/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086360 Building REAL300000086361 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086361' /scratch/stefan/7769667/working/building/REAL300000086361 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086361 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086361/0 /scratch/stefan/7769667/working/building/REAL300000086361 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/379 `/scratch/stefan/7769667/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(C)N=C1C1=CC=CC=C1Br)C(=O)[O-]) `REAL300000086361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086361 none CCC(NN=CC1=CN(C)N=C1C1=CC=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'Br', '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, 5, 5, 8, 8, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 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: [70, 49, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 49, 58, 58, 70, 70, 70, 70, 70, 49, 26, 9, 1, 2, 2, 2, 7, 7, 6, 7] 127 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 353 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086361 none CCC(NN=CC1=CN(C)N=C1C1=CC=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'Br', '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, 5, 5, 8, 8, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 107, 74, 30, 30, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 107, 125, 125, 127, 127, 127, 127, 127, 107, 74, 30, 7, 7, 7, 7, 1, 1, 1, 1] 127 rigid atoms, others: [34, 35, 36, 37, 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, 33]) total number of confs: 575 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086361 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086361 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086361/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086361 Building REAL300000086362 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086362' /scratch/stefan/7769667/working/building/REAL300000086362 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086362 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086362/0 /scratch/stefan/7769667/working/building/REAL300000086362 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/380 `/scratch/stefan/7769667/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC(C(F)(F)F)=CC=C1Br)C(=O)[O-]) `REAL300000086362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086362 none CCC(NN=C(C)C1=CC(C(F)(F)F)=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', '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, 5, 15, 15, 15, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 50, 33, 9, 9, 1, 9, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 50, 54, 54, 57, 57, 57, 57, 57, 50, 33, 9, 9, 9, 1, 1, 1] 57 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 233 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086362 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086362 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086362/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086362 Building REAL300000086363 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086363' /scratch/stefan/7769667/working/building/REAL300000086363 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086363 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086363/0 /scratch/stefan/7769667/working/building/REAL300000086363 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/381 `/scratch/stefan/7769667/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(N2C=CC(C(F)(F)F)=N2)C=C1C)C(=O)[O-]) `REAL300000086363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086363 none CCC(NN=CC1=CC=C(N2C=CC(C(F)(F)F)=N2)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [80, 72, 45, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 72, 80, 80, 80, 80, 80, 80, 80, 72, 45, 12, 1, 1, 7, 7, 1, 2, 2, 2] 105 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 19, 20, 21, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39, 40]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086363 none CCC(NN=CC1=CC=C(N2C=CC(C(F)(F)F)=N2)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 102, 73, 29, 29, 6, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 7, 7, 7, 102, 105, 105, 105, 105, 105, 105, 105, 102, 73, 29, 7, 7, 1, 1, 7, 7, 7, 7] 105 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 392 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086363 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086363 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086363/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086363 Building REAL300000086364 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086364' /scratch/stefan/7769667/working/building/REAL300000086364 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086364 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086364/0 /scratch/stefan/7769667/working/building/REAL300000086364 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/382 `/scratch/stefan/7769667/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CN(C)N=C1C1CCOCC1)C(=O)[O-]) `REAL300000086364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086364 none CCC(NN=C(C)C1=CN(C)N=C1C1CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 8, 5, 8, 1, 5, 5, 5, 12, 5, 5, 1, 11, 11, 7, 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, 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, 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, 22, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 22, 24, 24, 25, 25, 25, 25, 25, 22, 16, 9, 9, 9, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 37 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086364 none CCC(NN=C(C)C1=CN(C)N=C1C1CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 8, 5, 8, 1, 5, 5, 5, 12, 5, 5, 1, 11, 11, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 33, 28, 14, 14, 4, 14, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 33, 36, 36, 37, 37, 37, 37, 37, 33, 28, 14, 14, 14, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 37 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 44] 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, 35]) total number of confs: 141 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086364 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086364 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086364/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086364 Building REAL300000086365 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086365' /scratch/stefan/7769667/working/building/REAL300000086365 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086365 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086365/0 /scratch/stefan/7769667/working/building/REAL300000086365 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/383 `/scratch/stefan/7769667/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CN=C(NC(=O)C(C)(C)C)C=N1)C(=O)[O-]) `REAL300000086365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086365 none CCC(NN=C(C)C1=CN=C(NC(=O)C(C)(C)C)C=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [52, 40, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 1, 1, 40, 50, 50, 52, 52, 52, 52, 52, 40, 22, 8, 8, 8, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 61 rigid atoms, others: [33, 5, 7, 8, 9, 10, 11, 44, 18, 19] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 272 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086365 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086365 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086365/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086365 Building REAL300000086366 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086366' /scratch/stefan/7769667/working/building/REAL300000086366 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086366 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086366/0 /scratch/stefan/7769667/working/building/REAL300000086366 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/384 `/scratch/stefan/7769667/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C(=O)OC)=C(O)C=C1Cl)C(=O)[O-]) `REAL300000086366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086366 none CCC(NN=CC1=CC(C(=O)OC)=C(O)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 12, 5, 1, 12, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 5, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 8, 8, 8, 10, 10, 10, 10, 10, 8, 5, 3, 1, 3, 3, 3, 2, 1] 26 rigid atoms, others: [34, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086366 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086366 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086366/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086366 Building REAL300000086367 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086367' /scratch/stefan/7769667/working/building/REAL300000086367 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086367 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086367/0 /scratch/stefan/7769667/working/building/REAL300000086367 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/385 `/scratch/stefan/7769667/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(Br)C=CC=C1Br)C(=O)[O-]) `REAL300000086367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086367 none CCC(NN=CC1=C(Br)C=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 17, 1, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [33, 25, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 29, 29, 33, 33, 33, 33, 33, 25, 17, 5, 1, 1, 1] 34 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086367 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086367 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086367/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086367 Building REAL300000086368 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086368' /scratch/stefan/7769667/working/building/REAL300000086368 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086368 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086368/0 /scratch/stefan/7769667/working/building/REAL300000086368 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/386 `/scratch/stefan/7769667/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(Cl)N(C2=CC=CC=C2)N=C1)C(=O)[O-]) `REAL300000086368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086368 none CCC(NN=CC1=C(Cl)N(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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, 5, 5, 8, 8, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 7, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 10, 10, 10, 14, 14, 14, 14, 14, 10, 7, 4, 3, 3, 2, 3, 3, 1] 14 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 16, 17] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086368 none CCC(NN=CC1=C(Cl)N(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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, 5, 5, 8, 8, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 9, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 14, 14, 14, 14, 14, 10, 9, 5, 1, 1, 1, 1, 1, 3] 14 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 54 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086368 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086368 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086368/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086368 Building REAL300000086369 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086369' /scratch/stefan/7769667/working/building/REAL300000086369 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086369 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086369/0 /scratch/stefan/7769667/working/building/REAL300000086369 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/387 `/scratch/stefan/7769667/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(F)C=C(Br)C=C1F)C(=O)[O-]) `REAL300000086369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086369 none CCC(NN=CC1=C(F)C=C(Br)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 15, 1, 1, 17, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 31, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 32, 32, 43, 43, 43, 43, 43, 31, 25, 7, 1, 1] 43 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086369 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086369 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086369/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086369 Building REAL300000086370 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086370' /scratch/stefan/7769667/working/building/REAL300000086370 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086370 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086370/0 /scratch/stefan/7769667/working/building/REAL300000086370 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/388 `/scratch/stefan/7769667/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC(C#N)(C2=CC=CN=C2)CC1)C(=O)[O-]) `REAL300000086370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086370 none CCC(NN=C1CCC(C#N)(C2=CC=CN=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 1, 8, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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, 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: [49, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 11, 12, 12, 1, 1, 26, 39, 39, 49, 49, 49, 49, 49, 26, 7, 1, 1, 1, 1, 12, 12, 11, 12, 1, 1, 1, 1] 104 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 17, 18, 40, 39, 37, 29, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 280 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086370 none CCC(NN=C1CCC(C#N)(C2=CC=CN=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 1, 8, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [104, 91, 46, 12, 12, 12, 12, 12, 1, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 91, 102, 102, 104, 104, 104, 104, 104, 91, 46, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 12, 12] 104 rigid atoms, others: [33, 34, 35, 36, 8, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 457 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086370 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086370 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086370/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086370 Building REAL300000086371 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086371' /scratch/stefan/7769667/working/building/REAL300000086371 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086371 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086371/0 /scratch/stefan/7769667/working/building/REAL300000086371 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/389 `/scratch/stefan/7769667/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C(C)(C)OCC2=CC=CC=C2)=CC=C1F)C(=O)[O-]) `REAL300000086371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086371 none CCC(NN=CC1=CC(C(C)(C)OCC2=CC=CC=C2)=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 24, 11, 4, 4, 1, 1, 1, 1, 1, 11, 11, 11, 25, 31, 67, 67, 31, 67, 67, 1, 1, 1, 1, 24, 37, 37, 41, 41, 41, 41, 41, 24, 11, 4, 1, 11, 11, 11, 11, 11, 11, 31, 31, 67, 67, 31, 67, 67, 1, 1] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 49, 50, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 455 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086371 none CCC(NN=CC1=CC(C(C)(C)OCC2=CC=CC=C2)=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 144, 98, 98, 67, 67, 67, 40, 9, 40, 40, 3, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 197, 201, 201, 201, 201, 201, 201, 201, 197, 144, 98, 67, 41, 41, 41, 41, 41, 41, 3, 3, 1, 1, 1, 1, 1, 67, 67] 201 rigid atoms, others: [48, 45, 44, 13, 14, 15, 16, 17, 18, 19, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 49, 50]) total number of confs: 810 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086371 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086371 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086371/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086371 Building REAL300000086372 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086372' /scratch/stefan/7769667/working/building/REAL300000086372 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086372 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086372/0 /scratch/stefan/7769667/working/building/REAL300000086372 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/390 `/scratch/stefan/7769667/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCOC2=CC(Cl)=C(Cl)C=C21)C(=O)[O-]) `REAL300000086372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086372 none CCC(NN=C1CCOC2=CC(Cl)=C(Cl)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 12, 1, 1, 1, 16, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 18, 18, 23, 23, 23, 23, 23, 15, 7, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31] set([0, 1, 2, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 105 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086372 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086372 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086372/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086372 Building REAL300000086373 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086373' /scratch/stefan/7769667/working/building/REAL300000086373 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086373 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086373/0 /scratch/stefan/7769667/working/building/REAL300000086373 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/391 `/scratch/stefan/7769667/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C(=O)OC)=C(O)C=C1Br)C(=O)[O-]) `REAL300000086373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086373 none CCC(NN=CC1=CC(C(=O)OC)=C(O)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 12, 5, 1, 12, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 8, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 10, 10, 10, 12, 12, 12, 12, 12, 10, 8, 4, 1, 3, 3, 3, 2, 1] 28 rigid atoms, others: [34, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086373 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086373 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086373/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086373 Building REAL300000086374 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086374' /scratch/stefan/7769667/working/building/REAL300000086374 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086374 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086374/0 /scratch/stefan/7769667/working/building/REAL300000086374 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/392 `/scratch/stefan/7769667/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C(=O)[O-])C=C(Br)S1)C(=O)[O-]) `REAL300000086374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086374 none CCC(NN=CC1=C(C(=O)[O-])C=C(Br)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 17, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [40, 28, 18, 3, 3, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 28, 33, 33, 40, 40, 40, 40, 40, 28, 17, 3, 1] 41 rigid atoms, others: [5, 6, 7, 8, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086374 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086374 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086374/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086374 Building REAL300000086375 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086375' /scratch/stefan/7769667/working/building/REAL300000086375 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086375 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086375/0 /scratch/stefan/7769667/working/building/REAL300000086375 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/393 `/scratch/stefan/7769667/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C)C=C(C)C(Br)=C1C)C(=O)[O-]) `REAL300000086375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086375 none CCC(NN=CC1=C(C)C=C(C)C(Br)=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 5, 1, 1, 5, 1, 17, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 72, 54, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 74, 74, 95, 95, 95, 95, 95, 72, 54, 13, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2] 95 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086375 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086375 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086375/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086375 Building REAL300000086376 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086376' /scratch/stefan/7769667/working/building/REAL300000086376 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086376 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086376/0 /scratch/stefan/7769667/working/building/REAL300000086376 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/394 `/scratch/stefan/7769667/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC(F)=CC=C1Br)C(=O)[O-]) `REAL300000086376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086376 none CCC(NN=C(C)C1=CC(F)=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', '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, 15, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 45, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 45, 49, 49, 61, 61, 61, 61, 61, 45, 27, 9, 9, 9, 1, 1, 1] 61 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 269 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086376 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086376 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086376/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086376 Building REAL300000086377 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086377' /scratch/stefan/7769667/working/building/REAL300000086377 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086377 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086377/0 /scratch/stefan/7769667/working/building/REAL300000086377 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/395 `/scratch/stefan/7769667/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1(C(=O)OCC)CCC(NN=C(CC)C(=O)[O-])CC1) `REAL300000086377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086377 none CCOC(=O)C1(C(=O)OCC)CCC(NN=C(CC)C(=O)[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 11, 5, 1, 11, 12, 5, 5, 5, 5, 5, 8, 8, 1, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 4, 1, 4, 1, 1, 6, 6, 6, 18, 1, 1, 1, 1, 6, 8, 8, 20, 8, 14, 14, 1, 1, 13, 13, 13, 12, 12, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 20, 1, 1, 1, 1] 201 rigid atoms, others: [34, 3, 36, 5, 6, 47, 11, 12, 13, 14, 45, 48, 35, 46, 22, 23, 38, 37] set([0, 1, 2, 4, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086377 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086377 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086377/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086377 Building REAL300000086378 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086378' /scratch/stefan/7769667/working/building/REAL300000086378 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086378 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086378/0 /scratch/stefan/7769667/working/building/REAL300000086378 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/396 `/scratch/stefan/7769667/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(C(F)(F)C(F)(F)OC)C=C1)C(=O)[O-]) `REAL300000086378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086378 none CCC(NN=CC1=CC=C(C(F)(F)C(F)(F)OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'O.3', 'C.3', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 5, 15, 15, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [54, 38, 18, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 54, 1, 1, 38, 50, 50, 54, 54, 54, 54, 54, 38, 18, 3, 1, 1, 54, 54, 54, 1, 1] 201 rigid atoms, others: [32, 36, 5, 6, 7, 8, 9, 10, 18, 19, 37, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086378 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086378 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086378/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086378 Building REAL300000086379 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086379' /scratch/stefan/7769667/working/building/REAL300000086379 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086379 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086379/0 /scratch/stefan/7769667/working/building/REAL300000086379 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/397 `/scratch/stefan/7769667/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CC1CC1)C1=CC=CC(C(F)(F)F)=C1)C(=O)[O-]) `REAL300000086379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086379 none CCC(NN=C(CC1CC1)C1=CC=CC(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 80, 44, 17, 17, 3, 1, 1, 1, 1, 17, 71, 71, 71, 71, 71, 71, 71, 71, 71, 80, 107, 107, 115, 115, 115, 115, 115, 80, 44, 3, 3, 1, 1, 1, 1, 1, 71, 71, 71, 71] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40]) total number of confs: 677 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086379 none CCC(NN=C(CC1CC1)C1=CC=CC(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 126, 64, 13, 13, 1, 13, 47, 71, 71, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 126, 156, 156, 163, 163, 163, 163, 163, 126, 64, 47, 47, 71, 71, 71, 71, 71, 1, 1, 1, 1] 201 rigid atoms, others: [5, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 37] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1032 number of broken/clashed sets: 82 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086379 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086379 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086379/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086379 Building REAL300000086380 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086380' /scratch/stefan/7769667/working/building/REAL300000086380 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086380 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086380/0 /scratch/stefan/7769667/working/building/REAL300000086380 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/398 `/scratch/stefan/7769667/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(NC(=O)OC(C)(C)C)=C1)C(=O)[O-]) `REAL300000086380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086380 none CCC(NN=CC1=CC=CC(NC(=O)OC(C)(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 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, 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: [15, 10, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 16, 17, 17, 17, 1, 10, 12, 12, 15, 15, 15, 15, 15, 10, 6, 4, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1] 42 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 44, 19, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086380 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086380 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086380/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086380 Building REAL300000086381 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086381' /scratch/stefan/7769667/working/building/REAL300000086381 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086381 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086381/0 /scratch/stefan/7769667/working/building/REAL300000086381 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/399 `/scratch/stefan/7769667/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(OC)C=CC(Br)=C1F)C(=O)[O-]) `REAL300000086381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086381 none CCC(NN=CC1=C(OC)C=CC(Br)=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 12, 5, 1, 1, 1, 17, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 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 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [75, 59, 40, 13, 13, 1, 1, 1, 1, 4, 1, 1, 1, 1, 1, 1, 59, 71, 71, 75, 75, 75, 75, 75, 59, 39, 13, 4, 4, 4, 1, 1] 84 rigid atoms, others: [5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086381 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086381 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086381/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086381 Building REAL300000086382 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086382' /scratch/stefan/7769667/working/building/REAL300000086382 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086382 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086382/0 /scratch/stefan/7769667/working/building/REAL300000086382 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/400 `/scratch/stefan/7769667/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC2=C(S1)SC(C(=O)OC)=C2)C(=O)[O-]) `REAL300000086382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086382 none CCC(NN=CC1=CC2=C(S1)SC(C(=O)OC)=C2)C(=O)[O-] 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', 'S.3', 'S.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 14, 14, 1, 1, 11, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 2, 2, 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: [69, 57, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 1, 57, 62, 62, 69, 69, 69, 69, 69, 57, 30, 6, 1, 13, 13, 13, 1] 122 rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 29] set([0, 1, 2, 3, 4, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086382 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086382 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086382/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086382 Building REAL300000086383 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086383' /scratch/stefan/7769667/working/building/REAL300000086383 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086383 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086383/0 /scratch/stefan/7769667/working/building/REAL300000086383 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/401 `/scratch/stefan/7769667/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CC1=CC=CC=C1)CC1CCCCC1)C(=O)[O-]) `REAL300000086383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086383 none CCC(NN=C(CC1=CC=CC=C1)CC1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 121, 64, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 15, 45, 63, 63, 63, 63, 63, 121, 145, 145, 155, 155, 155, 155, 155, 121, 64, 4, 4, 1, 1, 1, 1, 1, 45, 45, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 952 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086383 none CCC(NN=C(CC1=CC=CC=C1)CC1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 87, 47, 15, 15, 6, 15, 45, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 1, 87, 111, 111, 122, 122, 122, 122, 122, 87, 47, 45, 45, 63, 63, 63, 63, 63, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [48, 45, 49, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 779 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086383 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086383 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086383/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086383 Building REAL300000086384 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086384' /scratch/stefan/7769667/working/building/REAL300000086384 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086384 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086384/0 /scratch/stefan/7769667/working/building/REAL300000086384 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/402 `/scratch/stefan/7769667/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1)C(=O)[O-]) `REAL300000086384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086384 none CCC(NN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [31, 17, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 27, 79, 79, 79, 79, 79, 79, 79, 17, 27, 27, 31, 31, 31, 31, 31, 17, 6, 4, 1, 1, 1, 1, 27, 27, 79, 79] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12] 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, 37, 38, 39, 40]) total number of confs: 339 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086384 none CCC(NN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [201, 167, 117, 97, 97, 79, 79, 79, 79, 79, 79, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 167, 201, 201, 201, 201, 201, 201, 201, 167, 117, 97, 79, 79, 79, 79, 9, 9, 1, 1] 201 rigid atoms, others: [39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 884 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086384 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086384 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086384/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086384 Building REAL300000086385 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086385' /scratch/stefan/7769667/working/building/REAL300000086385 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086385 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086385/0 /scratch/stefan/7769667/working/building/REAL300000086385 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/403 `/scratch/stefan/7769667/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC2=C(C)C=C(Br)C=C2N1)C(=O)[O-]) `REAL300000086385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086385 none CCC(NN=CC1=CC2=C(C)C=C(Br)C=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', '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, 5, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 17, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 39, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 42, 42, 47, 47, 47, 47, 47, 39, 23, 6, 1, 2, 2, 2, 1, 1, 1] 47 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086385 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086385 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086385/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086385 Building REAL300000086386 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086386' /scratch/stefan/7769667/working/building/REAL300000086386 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086386 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086386/0 /scratch/stefan/7769667/working/building/REAL300000086386 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/404 `/scratch/stefan/7769667/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC2=C(N1)C(Br)=CS2)C(=O)[O-]) `REAL300000086386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086386 none CCC(NN=CC1=CC2=C(N1)C(Br)=CS2)C(=O)[O-] 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', 'N.pl3', 'C.2', 'Br', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 17, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 41, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 45, 45, 57, 57, 57, 57, 57, 41, 27, 6, 1, 1, 1] 57 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086386 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086386 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086386/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086386 Building REAL300000086387 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086387' /scratch/stefan/7769667/working/building/REAL300000086387 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086387 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086387/0 /scratch/stefan/7769667/working/building/REAL300000086387 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/405 `/scratch/stefan/7769667/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(F)C=C(C(F)(F)F)C=C1Br)C(=O)[O-]) `REAL300000086387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086387 none CCC(NN=CC1=C(F)C=C(C(F)(F)F)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 68, 43, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 68, 76, 76, 81, 81, 81, 81, 81, 68, 43, 12, 1, 1] 81 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086387 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086387 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086387/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086387 Building REAL300000086388 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086388' /scratch/stefan/7769667/working/building/REAL300000086388 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086388 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086388/0 /scratch/stefan/7769667/working/building/REAL300000086388 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/406 `/scratch/stefan/7769667/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(F)C=C(C#N)C=C1Br)C(=O)[O-]) `REAL300000086388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086388 none CCC(NN=CC1=C(F)C=C(C#N)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 65, 44, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 69, 69, 92, 92, 92, 92, 92, 65, 44, 10, 1, 1] 92 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 387 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086388 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086388 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086388/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086388 Building REAL300000086389 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086389' /scratch/stefan/7769667/working/building/REAL300000086389 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086389 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086389/0 /scratch/stefan/7769667/working/building/REAL300000086389 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/407 `/scratch/stefan/7769667/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(Br)=C1C(=O)[O-])C(=O)[O-]) `REAL300000086389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086389 none CCC(NN=CC1=CC=CC(Br)=C1C(=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 1, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 15, 16, 16, 21, 21, 21, 21, 21, 15, 10, 4, 1, 1, 1] 21 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086389 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086389 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086389/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086389 Building REAL300000086390 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086390' /scratch/stefan/7769667/working/building/REAL300000086390 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086390 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086390/0 /scratch/stefan/7769667/working/building/REAL300000086390 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/408 `/scratch/stefan/7769667/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CN=C(C2=NC=CC=C2C)S1)C(=O)[O-]) `REAL300000086390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086390 none CCC(NN=C(C)C1=CN=C(C2=NC=CC=C2C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 1, 8, 1, 1, 1, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [16, 11, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 11, 11, 11, 16, 16, 16, 16, 16, 11, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7] 20 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 18] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086390 none CCC(NN=C(C)C1=CN=C(C2=NC=CC=C2C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 1, 8, 1, 1, 1, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 18, 17, 10, 10, 7, 10, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 20, 20, 20, 20, 20, 18, 17, 10, 10, 10, 7, 1, 1, 1, 2, 2, 2] 20 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 66 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086390 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086390 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086390/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086390 Building REAL300000086391 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086391' /scratch/stefan/7769667/working/building/REAL300000086391 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086391 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086391/0 /scratch/stefan/7769667/working/building/REAL300000086391 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/409 `/scratch/stefan/7769667/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C)C(OC)=C(C)C(C)=C1OC)C(=O)[O-]) `REAL300000086391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086391 none CCC(NN=CC1=C(C)C(OC)=C(C)C(C)=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 5, 1, 12, 5, 1, 5, 1, 5, 1, 12, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 3, 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, 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: [114, 75, 40, 12, 12, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 2, 75, 93, 93, 114, 114, 114, 114, 114, 75, 40, 12, 2, 2, 2, 3, 3, 3, 2, 2, 2, 2, 2, 2, 3, 3, 3] 147 rigid atoms, others: [5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 11, 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: 600 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086391 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086391 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086391/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086391 Building REAL300000086392 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086392' /scratch/stefan/7769667/working/building/REAL300000086392 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086392 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086392/0 /scratch/stefan/7769667/working/building/REAL300000086392 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/410 `/scratch/stefan/7769667/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(Cl)C(Br)=C1F)C(=O)[O-]) `REAL300000086392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086392 none CCC(NN=CC1=CC=C(Cl)C(Br)=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 17, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 40, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 41, 41, 51, 51, 51, 51, 51, 40, 29, 10, 1, 1] 51 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086392 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086392 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086392/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086392 Building REAL300000086393 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086393' /scratch/stefan/7769667/working/building/REAL300000086393 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086393 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086393/0 /scratch/stefan/7769667/working/building/REAL300000086393 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/411 `/scratch/stefan/7769667/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1OC1CCCCC1)C(=O)[O-]) `REAL300000086393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086393 none CCC(NN=CC1=CC=CC=C1OC1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [23, 14, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 24, 24, 24, 24, 24, 14, 15, 15, 23, 23, 23, 23, 23, 14, 8, 4, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 62 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 4, 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: 155 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086393 none CCC(NN=CC1=CC=CC=C1OC1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 52, 46, 37, 37, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 62, 62, 62, 62, 62, 52, 46, 37, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 62 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 44] 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]) total number of confs: 196 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086393 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086393 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086393/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086393 Building REAL300000086394 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086394' /scratch/stefan/7769667/working/building/REAL300000086394 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086394 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086394/0 /scratch/stefan/7769667/working/building/REAL300000086394 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/412 `/scratch/stefan/7769667/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(OC2=CC=CC(Cl)=C2)C=C1)C(=O)[O-]) `REAL300000086394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086394 none CCC(NN=CC1=CC=C(OC2=CC=CC(Cl)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 24, 11, 3, 3, 1, 1, 1, 1, 1, 1, 9, 37, 37, 37, 37, 37, 37, 1, 1, 24, 34, 34, 34, 34, 34, 34, 34, 24, 10, 3, 1, 1, 37, 37, 37, 37, 1, 1] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 38, 37, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086394 none CCC(NN=CC1=CC=C(OC2=CC=CC(Cl)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 190, 129, 76, 76, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 190, 190, 190, 201, 201, 201, 201, 201, 190, 129, 76, 37, 37, 1, 1, 1, 1, 37, 37] 201 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 775 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086394 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086394 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086394/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086394 Building REAL300000086395 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086395' /scratch/stefan/7769667/working/building/REAL300000086395 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086395 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086395/0 /scratch/stefan/7769667/working/building/REAL300000086395 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/413 `/scratch/stefan/7769667/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1COC1CCCCC1)C(=O)[O-]) `REAL300000086395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086395 none CCC(NN=CC1=CC=CC=C1COC1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 32, 26, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 30, 65, 65, 65, 65, 65, 32, 39, 39, 54, 54, 54, 54, 54, 32, 26, 12, 1, 1, 1, 1, 7, 7, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65] 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, 43, 44, 45, 46, 47]) total number of confs: 414 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086395 none CCC(NN=CC1=CC=CC=C1COC1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 187, 182, 141, 141, 65, 65, 65, 65, 65, 65, 20, 8, 1, 1, 1, 1, 1, 1, 1, 187, 201, 201, 201, 201, 201, 201, 201, 187, 182, 141, 65, 65, 65, 65, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 648 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086395 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086395 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086395/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086395 Building REAL300000086396 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086396' /scratch/stefan/7769667/working/building/REAL300000086396 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086396 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086396/0 /scratch/stefan/7769667/working/building/REAL300000086396 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/414 `/scratch/stefan/7769667/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1OCC1=CC=C(Cl)C=C1)C(=O)[O-]) `REAL300000086396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086396 none CCC(NN=CC1=CC=CC=C1OCC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'Cl', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 22, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 44, 88, 88, 88, 88, 88, 88, 22, 32, 32, 39, 39, 39, 39, 39, 22, 9, 4, 1, 1, 1, 1, 44, 44, 88, 88, 88, 88] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12] 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, 36, 37, 38, 39, 40, 41]) total number of confs: 420 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086396 none CCC(NN=CC1=CC=CC=C1OCC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'Cl', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 166, 137, 106, 106, 88, 88, 88, 87, 88, 88, 23, 3, 1, 1, 1, 1, 1, 1, 1, 1, 166, 201, 201, 201, 201, 201, 201, 201, 166, 137, 106, 88, 88, 88, 88, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 829 number of broken/clashed sets: 41 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086396 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086396 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086396/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086396 Building REAL300000086397 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086397' /scratch/stefan/7769667/working/building/REAL300000086397 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086397 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086397/0 /scratch/stefan/7769667/working/building/REAL300000086397 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/415 `/scratch/stefan/7769667/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(OC2=CC=CC(OC)=C2)C=C1)C(=O)[O-]) `REAL300000086397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086397 none CCC(NN=CC1=CC=C(OC2=CC=CC(OC)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 20, 9, 3, 3, 1, 1, 1, 1, 1, 1, 9, 37, 37, 37, 37, 37, 70, 37, 1, 1, 20, 29, 29, 32, 32, 32, 32, 32, 20, 9, 3, 1, 1, 37, 37, 37, 70, 70, 70, 37, 1, 1] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 19, 20, 41, 42] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086397 none CCC(NN=CC1=CC=C(OC2=CC=CC(OC)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 159, 97, 59, 59, 15, 9, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 2, 1, 37, 37, 159, 195, 195, 201, 201, 201, 201, 201, 159, 97, 59, 37, 37, 1, 1, 1, 3, 3, 3, 1, 37, 37] 201 rigid atoms, others: [34, 35, 36, 40, 10, 11, 12, 13, 14, 15, 16, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 41, 42]) total number of confs: 1083 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086397 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086397 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086397/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086397 Building REAL300000086398 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086398' /scratch/stefan/7769667/working/building/REAL300000086398 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086398 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086398/0 /scratch/stefan/7769667/working/building/REAL300000086398 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/416 `/scratch/stefan/7769667/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C12CCCC1CC(NN=C(CC)C(=O)[O-])CC2) `REAL300000086398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086398 none CCOC(=O)C12CCCC1CC(NN=C(CC)C(=O)[O-])CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 11, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 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, 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: [30, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 56, 14, 36, 36, 1, 1, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 56, 56, 56, 56, 56, 1, 1, 1, 1] 138 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42]) total number of confs: 357 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086398 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086398 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086398/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086398 Building REAL300000086399 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086399' /scratch/stefan/7769667/working/building/REAL300000086399 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086399 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086399/0 /scratch/stefan/7769667/working/building/REAL300000086399 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/417 `/scratch/stefan/7769667/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC2=C(Br)C=CC=C2N1)C(=O)[O-]) `REAL300000086399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086399 none CCC(NN=CC1=CC2=C(Br)C=CC=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 38, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 41, 41, 49, 49, 49, 49, 49, 38, 25, 7, 1, 1, 1, 1, 1] 49 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086399 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086399 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086399/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086399 Building REAL300000086400 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086400' /scratch/stefan/7769667/working/building/REAL300000086400 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086400 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086400/0 /scratch/stefan/7769667/working/building/REAL300000086400 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/418 `/scratch/stefan/7769667/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CN=C(C2=CC=CC=C2C)S1)C(=O)[O-]) `REAL300000086400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086400 none CCC(NN=C(C)C1=CN=C(C2=CC=CC=C2C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.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, 5, 5, 8, 8, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 10, 10, 1, 10, 10, 10, 1, 10, 10, 10, 15, 15, 15, 15, 15, 10, 10, 6, 6, 6, 1, 10, 10, 1, 10, 10, 10, 10] 28 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 18] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086400 none CCC(NN=C(C)C1=CN=C(C2=CC=CC=C2C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.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, 5, 5, 8, 8, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 26, 26, 18, 18, 10, 18, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 26, 26, 26, 28, 28, 28, 28, 28, 26, 26, 18, 18, 18, 10, 1, 1, 1, 1, 2, 2, 2] 28 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086400 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086400 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086400/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086400 Building REAL300000086401 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086401' /scratch/stefan/7769667/working/building/REAL300000086401 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086401 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086401/0 /scratch/stefan/7769667/working/building/REAL300000086401 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/419 `/scratch/stefan/7769667/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(OC2=CC=CC=C2OC)C=C1)C(=O)[O-]) `REAL300000086401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086401 none CCC(NN=CC1=CC=C(OC2=CC=CC=C2OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 25, 12, 3, 3, 1, 1, 1, 1, 1, 1, 9, 27, 27, 19, 27, 27, 27, 55, 1, 1, 25, 37, 37, 40, 40, 40, 40, 40, 25, 11, 3, 1, 1, 27, 27, 27, 27, 55, 55, 55, 1, 1] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 19, 20, 41, 42] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086401 none CCC(NN=CC1=CC=C(OC2=CC=CC=C2OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 172, 115, 55, 55, 27, 25, 27, 27, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 27, 27, 172, 186, 186, 199, 199, 199, 199, 199, 172, 115, 55, 27, 27, 1, 1, 1, 1, 4, 4, 4, 27, 27] 201 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 859 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086401 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086401 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086401/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086401 Building REAL300000086402 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086402' /scratch/stefan/7769667/working/building/REAL300000086402 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086402 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086402/0 /scratch/stefan/7769667/working/building/REAL300000086402 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/420 `/scratch/stefan/7769667/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C2=CC=CC=C2)N=C2N=CC=CN21)C(=O)[O-]) `REAL300000086402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086402 none CCC(NN=CC1=C(C2=CC=CC=C2)N=C2N=CC=CN21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', '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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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] 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: [19, 14, 8, 3, 3, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 14, 17, 17, 19, 19, 19, 19, 19, 14, 7, 3, 5, 5, 1, 5, 5, 1, 1, 1] 20 rigid atoms, others: [5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 39, 38, 37] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086402 none CCC(NN=CC1=C(C2=CC=CC=C2)N=C2N=CC=CN21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', '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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 17, 13, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 17, 20, 20, 20, 20, 20, 20, 20, 17, 13, 8, 1, 1, 1, 1, 1, 5, 5, 5] 20 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086402 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086402 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086402/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086402 Building REAL300000086403 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086403' /scratch/stefan/7769667/working/building/REAL300000086403 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086403 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086403/0 /scratch/stefan/7769667/working/building/REAL300000086403 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/421 `/scratch/stefan/7769667/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1CC1=CC=C(Cl)C=C1)C(=O)[O-]) `REAL300000086403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086403 none CCC(NN=CC1=CC=CC=C1CC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 59, 29, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 10, 19, 19, 19, 19, 19, 19, 59, 70, 70, 86, 86, 86, 86, 86, 59, 29, 12, 1, 1, 1, 1, 10, 10, 19, 19, 19, 19] 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]) total number of confs: 471 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086403 none CCC(NN=CC1=CC=CC=C1CC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 181, 138, 87, 87, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 181, 201, 201, 201, 201, 201, 201, 201, 181, 138, 87, 19, 19, 19, 19, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 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, 36]) total number of confs: 832 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086403 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086403 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086403/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086403 Building REAL300000086404 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086404' /scratch/stefan/7769667/working/building/REAL300000086404 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086404 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086404/0 /scratch/stefan/7769667/working/building/REAL300000086404 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/422 `/scratch/stefan/7769667/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(Br)C=CC=C1OC(F)(F)F)C(=O)[O-]) `REAL300000086404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086404 none CCC(NN=CC1=C(Br)C=CC=C1OC(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 17, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 81, 48, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 81, 118, 118, 127, 127, 127, 127, 127, 81, 48, 10, 1, 1, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 738 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086404 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086404 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086404/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086404 Building REAL300000086405 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086405' /scratch/stefan/7769667/working/building/REAL300000086405 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086405 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086405/0 /scratch/stefan/7769667/working/building/REAL300000086405 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/423 `/scratch/stefan/7769667/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(SC(F)(F)F)=C1)C(=O)[O-]) `REAL300000086405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086405 none CCC(NN=CC1=CC=CC(SC(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 14, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [21, 13, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 17, 17, 17, 1, 13, 13, 13, 21, 21, 21, 21, 21, 13, 9, 6, 1, 1, 1, 1] 58 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086405 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086405 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086405/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086405 Building REAL300000086406 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086406' /scratch/stefan/7769667/working/building/REAL300000086406 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086406 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086406/0 /scratch/stefan/7769667/working/building/REAL300000086406 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/424 `/scratch/stefan/7769667/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(S(=O)(=O)N(C)C)C=C1Br)C(=O)[O-]) `REAL300000086406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086406 none CCC(NN=CC1=CC=C(S(=O)(=O)N(C)C)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', '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, 14, 11, 11, 8, 5, 5, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [107, 74, 40, 10, 10, 1, 1, 1, 1, 1, 1, 9, 9, 9, 20, 20, 1, 1, 1, 74, 93, 93, 107, 107, 107, 107, 107, 74, 40, 10, 1, 1, 20, 20, 20, 20, 20, 20, 1] 196 rigid atoms, others: [5, 6, 7, 8, 9, 10, 16, 17, 18, 38, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 593 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086406 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086406 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086406/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086406 Building REAL300000086407 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086407' /scratch/stefan/7769667/working/building/REAL300000086407 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086407 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086407/0 /scratch/stefan/7769667/working/building/REAL300000086407 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/425 `/scratch/stefan/7769667/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(OCC2=CC=C(Cl)C=C2)=C1)C(=O)[O-]) `REAL300000086407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086407 none CCC(NN=CC1=CC=CC(OCC2=CC=C(Cl)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 81, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 15, 15, 15, 15, 15, 15, 1, 81, 110, 110, 128, 128, 128, 128, 128, 81, 41, 11, 1, 1, 1, 7, 7, 15, 15, 15, 15, 1] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 20, 41] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 697 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086407 none CCC(NN=CC1=CC=CC(OCC2=CC=C(Cl)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 133, 55, 55, 15, 15, 15, 15, 15, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 15, 191, 201, 201, 201, 201, 201, 201, 201, 191, 133, 55, 15, 15, 15, 4, 4, 1, 1, 1, 1, 15] 201 rigid atoms, others: [37, 38, 39, 40, 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, 36, 41]) total number of confs: 745 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086407 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086407 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086407/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086407 Building REAL300000086408 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086408' /scratch/stefan/7769667/working/building/REAL300000086408 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086408 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086408/0 /scratch/stefan/7769667/working/building/REAL300000086408 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/426 `/scratch/stefan/7769667/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C2C(=C1)CCC21OCCO1)C(=O)[O-]) `REAL300000086408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086408 none CCC(NN=CC1=CC=C2C(=C1)CCC21OCCO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 50, 32, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 58, 58, 58, 58, 58, 50, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 58 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086408 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086408 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086408/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086408 Building REAL300000086409 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086409' /scratch/stefan/7769667/working/building/REAL300000086409 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086409 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086409/0 /scratch/stefan/7769667/working/building/REAL300000086409 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/427 `/scratch/stefan/7769667/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(Br)C=C1OC(F)F)C(=O)[O-]) `REAL300000086409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086409 none CCC(NN=CC1=CC=C(Br)C=C1OC(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 1, 12, 5, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens 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, 53, 25, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 39, 39, 53, 79, 79, 91, 91, 91, 91, 91, 53, 25, 4, 1, 1, 1, 39] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 617 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086409 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086409 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086409/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086409 Building REAL300000086410 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086410' /scratch/stefan/7769667/working/building/REAL300000086410 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086410 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086410/0 /scratch/stefan/7769667/working/building/REAL300000086410 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/428 `/scratch/stefan/7769667/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CN=C(C2=CC=CC=N2)S1)C(=O)[O-]) `REAL300000086410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086410 none CCC(NN=C(C)C1=CN=C(C2=CC=CC=N2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.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, 5, 8, 8, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 9, 9, 8, 7, 4, 4, 4, 1, 1, 1, 1, 1] 9 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 37 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086410 none CCC(NN=C(C)C1=CN=C(C2=CC=CC=N2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.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, 5, 8, 8, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 8, 3, 3, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 9, 9, 8, 7, 4, 4, 4, 1, 1, 1, 1, 1] 9 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 27 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086410 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086410 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086410/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086410 Building REAL300000086411 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086411' /scratch/stefan/7769667/working/building/REAL300000086411 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086411 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086411/0 /scratch/stefan/7769667/working/building/REAL300000086411 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/429 `/scratch/stefan/7769667/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(OC)C=C(OC)C2=CC=C(Cl)N=C21)C(=O)[O-]) `REAL300000086411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086411 none CCC(NN=CC1=C(OC)C=C(OC)C2=CC=C(Cl)N=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 12, 5, 1, 1, 12, 5, 1, 1, 1, 1, 16, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [104, 72, 37, 12, 12, 1, 1, 1, 1, 3, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 1, 72, 93, 93, 104, 104, 104, 104, 104, 72, 37, 12, 3, 3, 3, 1, 4, 4, 4, 1, 1] 122 rigid atoms, others: [35, 5, 6, 7, 8, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 40, 39] set([0, 1, 2, 3, 4, 9, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 535 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086411 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086411 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086411/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086411 Building REAL300000086412 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086412' /scratch/stefan/7769667/working/building/REAL300000086412 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086412 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086412/0 /scratch/stefan/7769667/working/building/REAL300000086412 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/430 `/scratch/stefan/7769667/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(F)C=CC(Br)=C1OC)C(=O)[O-]) `REAL300000086412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086412 none CCC(NN=CC1=C(F)C=CC(Br)=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 15, 1, 1, 1, 17, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 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: [78, 63, 42, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 63, 68, 68, 78, 78, 78, 78, 78, 63, 42, 13, 1, 1, 3, 3, 3] 85 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086412 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086412 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086412/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086412 Building REAL300000086413 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086413' /scratch/stefan/7769667/working/building/REAL300000086413 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086413 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086413/0 /scratch/stefan/7769667/working/building/REAL300000086413 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/431 `/scratch/stefan/7769667/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C2OCCOC2=C(Br)S1)C(=O)[O-]) `REAL300000086413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086413 none CCC(NN=CC1=C2OCCOC2=C(Br)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 12, 5, 5, 12, 1, 1, 17, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 52, 38, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 53, 53, 65, 65, 65, 65, 65, 52, 37, 7, 1, 1, 1, 1] 65 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086413 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086413 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086413/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086413 Building REAL300000086414 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086414' /scratch/stefan/7769667/working/building/REAL300000086414 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086414 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086414/0 /scratch/stefan/7769667/working/building/REAL300000086414 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/432 `/scratch/stefan/7769667/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C)SC(C)=C1S(N)(=O)=O)C(=O)[O-]) `REAL300000086414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086414 none CCC(NN=CC1=C(C)SC(C)=C1S(N)(=O)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 5, 5, 8, 8, 1, 1, 1, 5, 14, 1, 5, 1, 14, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 2, 2, 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, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 3 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086414 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086414 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086414/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086414 Building REAL300000086415 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086415' /scratch/stefan/7769667/working/building/REAL300000086415 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086415 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086415/0 /scratch/stefan/7769667/working/building/REAL300000086415 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/433 `/scratch/stefan/7769667/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CN=C(C2=NC=CC=N2)N=C1C)C(=O)[O-]) `REAL300000086415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086415 none CCC(NN=C(C)C1=CN=C(C2=NC=CC=N2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 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 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [131, 101, 46, 10, 10, 1, 10, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 101, 121, 121, 131, 131, 131, 131, 131, 101, 46, 10, 10, 10, 1, 6, 1, 6, 2, 2, 2] 143 rigid atoms, others: [33, 5, 7, 8, 9, 10, 11, 17, 18, 19] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 643 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086415 none CCC(NN=C(C)C1=CN=C(C2=NC=CC=N2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 138, 110, 50, 47, 2, 48, 2, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 138, 143, 143, 145, 145, 145, 145, 145, 138, 110, 25, 50, 50, 12, 1, 1, 1, 13, 13, 13] 145 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 541 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086415 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086415 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086415/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086415 Building REAL300000086416 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086416' /scratch/stefan/7769667/working/building/REAL300000086416 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086416 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086416/0 /scratch/stefan/7769667/working/building/REAL300000086416 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/434 `/scratch/stefan/7769667/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(OC)C(OC)=C(S(N)(=O)=O)S1)C(=O)[O-]) `REAL300000086416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086416 none CCC(NN=CC1=C(OC)C(OC)=C(S(N)(=O)=O)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.3', 'C.3', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'S.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, 5, 5, 8, 8, 1, 1, 1, 12, 5, 1, 12, 5, 1, 14, 8, 11, 11, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 4, 6, 6, 7, 7, 2, 2, 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: [60, 39, 16, 6, 6, 1, 1, 1, 1, 6, 1, 1, 5, 1, 1, 4, 4, 4, 1, 39, 54, 54, 60, 60, 60, 60, 60, 39, 16, 6, 7, 7, 7, 5, 5, 5, 5, 5] 149 rigid atoms, others: [5, 6, 7, 8, 10, 11, 13, 14, 18] set([0, 1, 2, 3, 4, 9, 12, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 351 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086416 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086416 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086416/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086416 Building REAL300000086417 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086417' /scratch/stefan/7769667/working/building/REAL300000086417 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086417 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086417/0 /scratch/stefan/7769667/working/building/REAL300000086417 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/435 `/scratch/stefan/7769667/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CNC2=CC(Cl)=C(OC)C=C12)C(=O)[O-]) `REAL300000086417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086417 none CCC(NN=CC1=CNC2=CC(Cl)=C(OC)C=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 16, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 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 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [89, 67, 33, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 67, 83, 83, 89, 89, 89, 89, 89, 67, 33, 7, 1, 1, 1, 4, 4, 4, 1] 96 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 33, 32, 34, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 429 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086417 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086417 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086417/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086417 Building REAL300000086418 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086418' /scratch/stefan/7769667/working/building/REAL300000086418 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086418 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086418/0 /scratch/stefan/7769667/working/building/REAL300000086418 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/436 `/scratch/stefan/7769667/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC(=O)NC2=CC=C(Cl)C=C21)C(=O)[O-]) `REAL300000086418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086418 none CCC(NN=C1CCC(=O)NC2=CC=C(Cl)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 17, 17, 19, 19, 19, 19, 19, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1] 19 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 2, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086418 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086418 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086418/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086418 Building REAL300000086419 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086419' /scratch/stefan/7769667/working/building/REAL300000086419 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086419 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086419/0 /scratch/stefan/7769667/working/building/REAL300000086419 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/437 `/scratch/stefan/7769667/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC(CC)C(=O)[O-])C1=CC=C(Br)C=C1C) `REAL300000086419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086419 none CCC(=NNC(CC)C(=O)[O-])C1=CC=C(Br)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [18, 9, 1, 9, 9, 34, 58, 83, 58, 68, 68, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 34, 58, 83, 83, 83, 83, 83, 1, 1, 1, 2, 2, 2] 88 rigid atoms, others: [32, 33, 2, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 435 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086419 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086419 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086419/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086419 Building REAL300000086420 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086420' /scratch/stefan/7769667/working/building/REAL300000086420 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086420 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086420/0 /scratch/stefan/7769667/working/building/REAL300000086420 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/438 `/scratch/stefan/7769667/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(F)C=CC(C)=C1Br)C(=O)[O-]) `REAL300000086420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086420 none CCC(NN=CC1=C(F)C=CC(C)=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', '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, 15, 1, 1, 1, 5, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 61, 44, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 65, 65, 82, 82, 82, 82, 82, 61, 44, 11, 1, 1, 2, 2, 2] 82 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086420 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086420 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086420/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086420 Building REAL300000086421 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086421' /scratch/stefan/7769667/working/building/REAL300000086421 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086421 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086421/0 /scratch/stefan/7769667/working/building/REAL300000086421 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/439 `/scratch/stefan/7769667/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1OCCC1CCCCC1)C(=O)[O-]) `REAL300000086421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086421 none CCC(NN=CC1=CC=CC=C1OCCC1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 31, 53, 87, 87, 87, 87, 87, 18, 24, 24, 24, 24, 24, 24, 24, 18, 9, 4, 1, 1, 1, 1, 31, 31, 65, 65, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12] 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 523 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086421 none CCC(NN=CC1=CC=CC=C1OCCC1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 142, 112, 112, 87, 87, 87, 87, 87, 87, 27, 6, 4, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 142, 112, 87, 87, 87, 87, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [48, 50, 49, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 705 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086421 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086421 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086421/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086421 Building REAL300000086422 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086422' /scratch/stefan/7769667/working/building/REAL300000086422 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086422 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086422/0 /scratch/stefan/7769667/working/building/REAL300000086422 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/440 `/scratch/stefan/7769667/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC(C2=CC=C([N+](=O)[O-])C=C2)C1(C)C)C(=O)[O-]) `REAL300000086422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086422 none CCC(NN=C1CC(C2=CC=C([N+](=O)[O-])C=C2)C1(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 20, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 3, 1, 1, 1, 20, 22, 22, 24, 24, 24, 24, 24, 20, 7, 1, 1, 1, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2] 24 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 17, 18, 19, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086422 none CCC(NN=C1CC(C2=CC=C([N+](=O)[O-])C=C2)C1(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 12, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3] 24 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 90 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086422 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086422 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086422/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086422 Building REAL300000086423 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086423' /scratch/stefan/7769667/working/building/REAL300000086423 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086423 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086423/0 /scratch/stefan/7769667/working/building/REAL300000086423 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/441 `/scratch/stefan/7769667/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(OCC2CCCO2)C(OC)=C1)C(=O)[O-]) `REAL300000086423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086423 none CCC(NN=CC1=CC=C(OCC2CCCO2)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 1, 12, 5, 1, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 29, 17, 6, 6, 1, 1, 1, 1, 1, 1, 10, 38, 65, 65, 65, 65, 1, 1, 3, 1, 29, 35, 35, 36, 36, 36, 36, 36, 29, 16, 6, 1, 1, 38, 38, 65, 65, 65, 65, 65, 65, 65, 4, 4, 4, 1] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 46, 17, 18, 20] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 385 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086423 none CCC(NN=CC1=CC=C(OCC2CCCO2)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 1, 12, 5, 1, 1, 11, 11, 7, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 145, 116, 116, 65, 37, 65, 65, 25, 7, 1, 1, 1, 1, 1, 1, 65, 65, 98, 65, 195, 199, 199, 201, 201, 201, 201, 201, 195, 145, 116, 65, 65, 7, 7, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 65] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46]) total number of confs: 896 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086423 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086423 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086423/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086423 Building REAL300000086424 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086424' /scratch/stefan/7769667/working/building/REAL300000086424 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086424 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086424/0 /scratch/stefan/7769667/working/building/REAL300000086424 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/442 `/scratch/stefan/7769667/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(F)C=CC=C1OCC(F)(F)F)C(=O)[O-]) `REAL300000086424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086424 none CCC(NN=CC1=C(F)C=CC=C1OCC(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', '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, 15, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 63, 28, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 40, 40, 40, 40, 63, 76, 76, 93, 93, 93, 93, 91, 63, 28, 12, 1, 1, 1, 40, 40] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 582 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086424 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086424 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086424/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086424 Building REAL300000086425 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086425' /scratch/stefan/7769667/working/building/REAL300000086425 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086425 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086425/0 /scratch/stefan/7769667/working/building/REAL300000086425 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/443 `/scratch/stefan/7769667/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=NC(Br)=CC=C1OC)C(=O)[O-]) `REAL300000086425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086425 none CCC(NN=CC1=NC(Br)=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [61, 54, 33, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 54, 58, 58, 61, 61, 61, 61, 61, 54, 33, 10, 1, 1, 4, 4, 4] 76 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086425 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086425 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086425/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086425 Building REAL300000086426 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086426' /scratch/stefan/7769667/working/building/REAL300000086426 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086426 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086426/0 /scratch/stefan/7769667/working/building/REAL300000086426 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/444 `/scratch/stefan/7769667/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC(CC)C(=O)[O-])C(C)C1=CC=CC(Br)=C1) `REAL300000086426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086426 none CCC(=NNC(CC)C(=O)[O-])C(C)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 8, 8, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 34, 11, 34, 34, 96, 139, 179, 139, 171, 171, 1, 11, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 96, 139, 179, 179, 179, 179, 179, 11, 11, 11, 11, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 987 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086426 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086426 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086426/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086426 Building REAL300000086427 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086427' /scratch/stefan/7769667/working/building/REAL300000086427 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086427 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086427/0 /scratch/stefan/7769667/working/building/REAL300000086427 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/445 `/scratch/stefan/7769667/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CC1=CC=C(F)C=C1)C1=NC=CN1C)C(=O)[O-]) `REAL300000086427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086427 none CCC(NN=C(CC1=CC=C(F)C=C1)C1=NC=CN1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [86, 66, 43, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 1, 19, 37, 37, 37, 37, 37, 66, 80, 80, 86, 86, 86, 86, 86, 66, 43, 4, 4, 1, 1, 1, 1, 37, 37, 37, 37, 37] 87 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39, 40]) total number of confs: 444 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086427 none CCC(NN=C(CC1=CC=C(F)C=C1)C1=NC=CN1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 10, 5, 5, 1, 5, 30, 37, 37, 34, 36, 37, 37, 1, 1, 1, 1, 1, 1, 19, 26, 26, 28, 28, 28, 28, 28, 19, 10, 30, 30, 37, 37, 37, 37, 1, 1, 2, 2, 2] 87 rigid atoms, others: [36, 5, 14, 15, 16, 17, 18, 19, 37] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 265 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086427 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086427 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086427/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086427 Building REAL300000086428 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086428' /scratch/stefan/7769667/working/building/REAL300000086428 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086428 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086428/0 /scratch/stefan/7769667/working/building/REAL300000086428 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/446 `/scratch/stefan/7769667/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(C2=CN=C(C(F)F)S2)C=C1)C(=O)[O-]) `REAL300000086428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086428 none CCC(NN=CC1=CC=C(C2=CN=C(C(F)F)S2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'S.3', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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] 0 hydrogens 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, 34, 16, 3, 3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 83, 83, 12, 1, 1, 34, 48, 48, 55, 55, 55, 55, 55, 34, 15, 3, 1, 1, 12, 83, 1, 1] 201 rigid atoms, others: [32, 35, 36, 5, 6, 7, 8, 9, 10, 18, 19, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 553 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086428 none CCC(NN=CC1=CC=C(C2=CN=C(C(F)F)S2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'S.3', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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] 0 hydrogens 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, 128, 67, 13, 12, 1, 1, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 142, 159, 159, 161, 161, 161, 160, 162, 126, 67, 12, 13, 13, 1, 12, 13, 13] 201 rigid atoms, others: [33, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 792 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086428 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086428 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086428/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086428 Building REAL300000086429 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086429' /scratch/stefan/7769667/working/building/REAL300000086429 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086429 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086429/0 /scratch/stefan/7769667/working/building/REAL300000086429 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/447 `/scratch/stefan/7769667/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC(C)=CC(Br)=C1O)C(=O)[O-]) `REAL300000086429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086429 none CCC(NN=C(C)C1=CC(C)=CC(Br)=C1O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 5, 1, 1, 17, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [68, 53, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 57, 57, 68, 68, 68, 68, 68, 53, 34, 9, 9, 9, 1, 2, 2, 2, 1, 2] 136 rigid atoms, others: [33, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34]) total number of confs: 301 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086429 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086429/1 /scratch/stefan/7769667/working/building/REAL300000086429 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/448 `/scratch/stefan/7769667/working/3D/448' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC(C)=CC(Br)=C1[O-])C(=O)[O-]) `REAL300000086429.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086429 none CCC(NN=C(C)C1=CC(C)=CC(Br)=C1[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.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, 5, 8, 8, 1, 5, 1, 1, 1, 5, 1, 1, 17, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 22, 22, 27, 27, 27, 27, 27, 18, 11, 3, 3, 3, 1, 2, 2, 2, 1] 27 rigid atoms, others: [33, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086429 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086429 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086429/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086429/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086429 Building REAL300000086430 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086430' /scratch/stefan/7769667/working/building/REAL300000086430 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086430 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086430/0 /scratch/stefan/7769667/working/building/REAL300000086430 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/449 `/scratch/stefan/7769667/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(Br)C=CC2=C1OCO2)C(=O)[O-]) `REAL300000086430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086430 none CCC(NN=CC1=C(Br)C=CC2=C1OCO2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 17, 1, 1, 1, 1, 12, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 49, 35, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 54, 54, 71, 71, 71, 71, 71, 49, 35, 10, 1, 1, 1, 1] 71 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086430 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086430 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086430/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086430 Building REAL300000086431 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086431' /scratch/stefan/7769667/working/building/REAL300000086431 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086431 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086431/0 /scratch/stefan/7769667/working/building/REAL300000086431 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/450 `/scratch/stefan/7769667/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(OCC2=CC=CC=C2)N(C)N=C1C)C(=O)[O-]) `REAL300000086431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086431 none CCC(NN=CC1=C(OCC2=CC=CC=C2)N(C)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.2', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 8, 1, 5, 1, 11, 11, 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, 4, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 34, 21, 10, 10, 1, 1, 1, 1, 8, 33, 67, 67, 39, 67, 67, 1, 1, 1, 1, 1, 34, 39, 39, 57, 57, 57, 57, 56, 34, 21, 10, 33, 33, 67, 67, 67, 67, 67, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [5, 6, 7, 8, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 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: 547 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086431 none CCC(NN=CC1=C(OCC2=CC=CC=C2)N(C)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.2', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 8, 1, 5, 1, 11, 11, 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, 4, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 175, 137, 137, 67, 67, 20, 3, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 191, 201, 201, 201, 201, 201, 201, 201, 191, 175, 137, 3, 3, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67] 201 rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44]) total number of confs: 652 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086431 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086431 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086431/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086431 Building REAL300000086432 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086432' /scratch/stefan/7769667/working/building/REAL300000086432 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086432 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086432/0 /scratch/stefan/7769667/working/building/REAL300000086432 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/451 `/scratch/stefan/7769667/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC(C(=O)OC)C2=CC=CC=C21)C(=O)[O-]) `REAL300000086432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086432 none CCC(NN=C1CCC(C(=O)OC)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 5, 3, 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] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [19, 14, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 14, 16, 16, 19, 19, 19, 19, 19, 14, 7, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1] 23 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 37, 38, 39, 40] set([0, 1, 2, 35, 36, 10, 11, 12, 34, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 94 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086432 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086432 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086432/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086432 Building REAL300000086433 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086433' /scratch/stefan/7769667/working/building/REAL300000086433 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086433 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086433/0 /scratch/stefan/7769667/working/building/REAL300000086433 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/452 `/scratch/stefan/7769667/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC(CC)C(=O)[O-])C1=CC(Cl)=CC2=C1OCC2) `REAL300000086433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086433 none CCC(=NNC(CC)C(=O)[O-])C1=CC(Cl)=CC2=C1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 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 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [35, 12, 1, 12, 12, 55, 99, 126, 99, 114, 114, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 55, 99, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 1] 144 rigid atoms, others: [33, 2, 34, 36, 37, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 38] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 678 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086433 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086433 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086433/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086433 Building REAL300000086434 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086434' /scratch/stefan/7769667/working/building/REAL300000086434 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086434 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086434/0 /scratch/stefan/7769667/working/building/REAL300000086434 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/453 `/scratch/stefan/7769667/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(C2=CC=CC(Cl)=C2)N=C1)C(=O)[O-]) `REAL300000086434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086434 none CCC(NN=CC1=CN(C2=CC=CC(Cl)=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 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: [14, 11, 8, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 11, 11, 11, 14, 14, 14, 14, 14, 11, 8, 5, 1, 2, 2, 2, 2, 1] 21 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086434 none CCC(NN=CC1=CN(C2=CC=CC(Cl)=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.2', '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, 5, 5, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 13, 8, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 17, 17, 17, 21, 21, 21, 21, 21, 17, 13, 8, 2, 1, 1, 1, 1, 2] 21 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086434 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086434 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086434/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086434 Building REAL300000086435 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086435' /scratch/stefan/7769667/working/building/REAL300000086435 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086435 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086435/0 /scratch/stefan/7769667/working/building/REAL300000086435 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/454 `/scratch/stefan/7769667/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(Br)C=C(C(F)(F)F)S1)C(=O)[O-]) `REAL300000086435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086435 none CCC(NN=CC1=C(Br)C=C(C(F)(F)F)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 60, 40, 10, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 60, 62, 62, 76, 76, 76, 76, 76, 60, 39, 10, 1] 76 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 15, 27] set([0, 1, 2, 3, 4, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 306 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086435 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086435 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086435/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086435 Building REAL300000086436 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086436' /scratch/stefan/7769667/working/building/REAL300000086436 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086436 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086436/0 /scratch/stefan/7769667/working/building/REAL300000086436 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/455 `/scratch/stefan/7769667/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=NC(C#N)=CC=C1Br)C(=O)[O-]) `REAL300000086436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086436 none CCC(NN=CC1=NC(C#N)=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 71, 46, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 77, 77, 95, 95, 95, 95, 95, 71, 46, 11, 1, 1] 95 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 400 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086436 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086436 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086436/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086436 Building REAL300000086437 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086437' /scratch/stefan/7769667/working/building/REAL300000086437 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086437 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086437/0 /scratch/stefan/7769667/working/building/REAL300000086437 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/456 `/scratch/stefan/7769667/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(Br)C=C1OC1CC1)C(=O)[O-]) `REAL300000086437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086437 none CCC(NN=CC1=CC=C(Br)C=C1OC1CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 45, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 41, 41, 45, 59, 59, 78, 78, 78, 78, 78, 45, 19, 6, 1, 1, 1, 41, 41, 41, 41, 41] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 491 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086437 none CCC(NN=CC1=CC=C(Br)C=C1OC1CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 160, 133, 78, 78, 41, 41, 41, 41, 41, 41, 41, 11, 1, 1, 1, 1, 160, 175, 175, 201, 201, 201, 201, 201, 160, 133, 78, 41, 41, 41, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 795 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086437 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086437 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086437/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086437 Building REAL300000086438 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086438' /scratch/stefan/7769667/working/building/REAL300000086438 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086438 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086438/0 /scratch/stefan/7769667/working/building/REAL300000086438 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/457 `/scratch/stefan/7769667/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(Cl)=C1C(F)(F)F)C(=O)[O-]) `REAL300000086438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086438 none CCC(NN=CC1=CC=CC(Cl)=C1C(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', '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, 16, 1, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 49, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 49, 52, 52, 60, 60, 60, 60, 60, 49, 30, 7, 1, 1, 1] 60 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 249 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086438 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086438 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086438/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086438 Building REAL300000086439 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086439' /scratch/stefan/7769667/working/building/REAL300000086439 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086439 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086439/0 /scratch/stefan/7769667/working/building/REAL300000086439 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/458 `/scratch/stefan/7769667/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(F)C=CC(Br)=C1Cl)C(=O)[O-]) `REAL300000086439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086439 none CCC(NN=CC1=C(F)C=CC(Br)=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 15, 1, 1, 1, 17, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [84, 63, 45, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 68, 68, 84, 84, 84, 84, 84, 63, 45, 12, 1, 1] 84 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086439 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086439 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086439/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086439 Building REAL300000086440 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086440' /scratch/stefan/7769667/working/building/REAL300000086440 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086440 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086440/0 /scratch/stefan/7769667/working/building/REAL300000086440 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/459 `/scratch/stefan/7769667/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=C([O-])C=C1F)C(=O)[O-]) `REAL300000086440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086440 none CCC(NN=CC1=CC(Br)=C([O-])C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 12, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 30, 22, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 31, 31, 38, 38, 38, 38, 38, 30, 21, 8, 1, 1] 38 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086440 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086440/1 /scratch/stefan/7769667/working/building/REAL300000086440 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/460 `/scratch/stefan/7769667/working/3D/460' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=C(O)C=C1F)C(=O)[O-]) `REAL300000086440.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086440 none CCC(NN=CC1=CC(Br)=C(O)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 12, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [51, 38, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 39, 39, 51, 51, 51, 51, 51, 38, 24, 8, 1, 2, 1] 102 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 28] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086440 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086440 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086440/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086440/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086440 Building REAL300000086441 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086441' /scratch/stefan/7769667/working/building/REAL300000086441 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086441 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086441/0 /scratch/stefan/7769667/working/building/REAL300000086441 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/461 `/scratch/stefan/7769667/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=CC2=CC=CN=C12)C(=O)[O-]) `REAL300000086441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086441 none CCC(NN=CC1=CC(Br)=CC2=CC=CN=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 26, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 32, 32, 32, 32, 32, 26, 18, 4, 1, 1, 1, 1, 1] 32 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086441 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086441 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086441/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086441 Building REAL300000086442 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086442' /scratch/stefan/7769667/working/building/REAL300000086442 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086442 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086442/0 /scratch/stefan/7769667/working/building/REAL300000086442 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/462 `/scratch/stefan/7769667/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=NN(CC(F)(F)F)C=C1Br)C(=O)[O-]) `REAL300000086442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086442 none CCC(NN=CC1=NN(CC(F)(F)F)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [82, 55, 28, 11, 11, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 1, 55, 63, 63, 82, 82, 82, 82, 82, 55, 28, 11, 9, 9, 1] 147 rigid atoms, others: [5, 6, 7, 8, 9, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086442 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086442 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086442/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086442 Building REAL300000086443 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086443' /scratch/stefan/7769667/working/building/REAL300000086443 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086443 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086443/0 /scratch/stefan/7769667/working/building/REAL300000086443 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/463 `/scratch/stefan/7769667/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=NN(C2=CC=CC=C2)N=C1C)C(=O)[O-]) `REAL300000086443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086443 none CCC(NN=C(C)C1=NN(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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, 5, 5, 8, 8, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 11, 3, 3, 1, 3, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 15, 16, 16, 16, 16, 16, 16, 16, 15, 11, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2] 16 rigid atoms, others: [5, 7, 8, 9, 10, 16, 17, 18] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 82 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086443 none CCC(NN=C(C)C1=NN(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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, 5, 5, 8, 8, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 12, 4, 4, 2, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 16, 16, 16, 16, 16, 16, 16, 15, 12, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2] 16 rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 59 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086443 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086443 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086443/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086443 Building REAL300000086444 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086444' /scratch/stefan/7769667/working/building/REAL300000086444 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086444 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086444/0 /scratch/stefan/7769667/working/building/REAL300000086444 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/464 `/scratch/stefan/7769667/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(Br)C(Cl)=C1F)C(=O)[O-]) `REAL300000086444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086444 none CCC(NN=CC1=CC=C(Br)C(Cl)=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 17, 1, 16, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 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, 40, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 41, 41, 49, 49, 49, 49, 49, 40, 29, 10, 1, 1] 49 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086444 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086444 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086444/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086444 Building REAL300000086445 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086445' /scratch/stefan/7769667/working/building/REAL300000086445 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086445 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086445/0 /scratch/stefan/7769667/working/building/REAL300000086445 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/465 `/scratch/stefan/7769667/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(OC)=C1Br)C(=O)[O-]) `REAL300000086445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086445 none CCC(NN=CC1=CC=CC(OC)=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Br', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 10, 10, 10, 15, 15, 15, 15, 15, 10, 9, 4, 1, 1, 1, 4, 4, 4] 16 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 13, 14, 26, 27, 28] set([0, 1, 2, 3, 4, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086445 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086445 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086445/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086445 Building REAL300000086446 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086446' /scratch/stefan/7769667/working/building/REAL300000086446 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086446 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086446/0 /scratch/stefan/7769667/working/building/REAL300000086446 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/466 `/scratch/stefan/7769667/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1C(=O)NC2=C(C(=O)OC)C=C(Br)C=C12)C(=O)[O-]) `REAL300000086446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086446 none CCC(NN=C1C(=O)NC2=C(C(=O)OC)C=C(Br)C=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 1, 1, 1, 11, 12, 5, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 5, 3, 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 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [26, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 1, 1, 1, 1, 1, 19, 23, 23, 26, 26, 26, 26, 26, 19, 6, 1, 12, 12, 12, 1, 1] 62 rigid atoms, others: [35, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 33, 32, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086446 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086446 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086446/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086446 Building REAL300000086447 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086447' /scratch/stefan/7769667/working/building/REAL300000086447 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086447 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086447/0 /scratch/stefan/7769667/working/building/REAL300000086447 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/467 `/scratch/stefan/7769667/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=C(OC)C=C1F)C(=O)[O-]) `REAL300000086447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086447 none CCC(NN=CC1=CC(Br)=C(OC)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 12, 5, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 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: [72, 56, 34, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 56, 59, 59, 72, 72, 72, 72, 72, 56, 33, 10, 1, 4, 4, 4, 1] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 27, 31] set([0, 1, 2, 3, 4, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 309 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086447 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086447 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086447/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086447 Building REAL300000086448 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086448' /scratch/stefan/7769667/working/building/REAL300000086448 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086448 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086448/0 /scratch/stefan/7769667/working/building/REAL300000086448 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/468 `/scratch/stefan/7769667/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C([N+](=O)[O-])C(OC2CC2)=C1)C(=O)[O-]) `REAL300000086448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086448 none CCC(NN=CC1=CC=C([N+](=O)[O-])C(OC2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 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: [90, 59, 32, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 8, 24, 24, 1, 59, 76, 76, 90, 90, 90, 90, 90, 59, 32, 11, 1, 1, 24, 24, 24, 24, 24, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 13, 14, 18, 37, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 507 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086448 none CCC(NN=CC1=CC=C([N+](=O)[O-])C(OC2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 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: [201, 176, 159, 85, 85, 24, 24, 24, 24, 24, 24, 24, 24, 9, 1, 1, 1, 1, 24, 176, 201, 201, 201, 201, 201, 201, 201, 176, 159, 85, 24, 24, 1, 1, 1, 1, 1, 24] 201 rigid atoms, others: [32, 33, 34, 35, 36, 14, 15, 16, 17] 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, 30, 31, 37]) total number of confs: 767 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086448 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086448 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086448/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086448 Building REAL300000086449 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086449' /scratch/stefan/7769667/working/building/REAL300000086449 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086449 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086449/0 /scratch/stefan/7769667/working/building/REAL300000086449 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/469 `/scratch/stefan/7769667/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=CC(Cl)=C1F)C(=O)[O-]) `REAL300000086449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086449 none CCC(NN=CC1=CC(Br)=CC(Cl)=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 16, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 38, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 39, 39, 49, 49, 49, 49, 49, 38, 28, 8, 1, 1] 49 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086449 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086449 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086449/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086449 Building REAL300000086450 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086450' /scratch/stefan/7769667/working/building/REAL300000086450 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086450 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086450/0 /scratch/stefan/7769667/working/building/REAL300000086450 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/470 `/scratch/stefan/7769667/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(F)C(C(F)(F)F)=C1Cl)C(=O)[O-]) `REAL300000086450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086450 none CCC(NN=CC1=CC=C(F)C(C(F)(F)F)=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 38, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 38, 39, 39, 43, 43, 43, 43, 43, 38, 23, 7, 1, 1] 43 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086450 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086450 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086450/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086450 Building REAL300000086451 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086451' /scratch/stefan/7769667/working/building/REAL300000086451 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086451 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086451/0 /scratch/stefan/7769667/working/building/REAL300000086451 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/471 `/scratch/stefan/7769667/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C)=CC(Br)=C1F)C(=O)[O-]) `REAL300000086451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086451 none CCC(NN=CC1=CC(C)=CC(Br)=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 5, 1, 1, 17, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 36, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 37, 37, 47, 47, 47, 47, 47, 36, 25, 8, 1, 2, 2, 2, 1] 47 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 30] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086451 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086451 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086451/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086451 Building REAL300000086452 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086452' /scratch/stefan/7769667/working/building/REAL300000086452 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086452 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086452/0 /scratch/stefan/7769667/working/building/REAL300000086452 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/472 `/scratch/stefan/7769667/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCOC2=CC=C(C(=O)OC)C=C21)C(=O)[O-]) `REAL300000086452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086452 none CCC(NN=C1CCOC2=CC=C(C(=O)OC)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 5, 12, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 5, 3, 7, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [39, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 1, 1, 23, 33, 33, 39, 39, 39, 39, 39, 23, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 1] 71 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 38, 29, 30, 31] set([0, 1, 2, 35, 36, 37, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 223 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086452 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086452 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086452/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086452 Building REAL300000086453 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086453' /scratch/stefan/7769667/working/building/REAL300000086453 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086453 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086453/0 /scratch/stefan/7769667/working/building/REAL300000086453 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/473 `/scratch/stefan/7769667/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC2=C1C=CC(Br)=C2F)C(=O)[O-]) `REAL300000086453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086453 none CCC(NN=C1CCC2=C1C=CC(Br)=C2F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 17, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 13, 13, 13, 13, 13, 8, 4, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 57 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086453 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086453 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086453/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086453 Building REAL300000086454 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086454' /scratch/stefan/7769667/working/building/REAL300000086454 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086454 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086454/0 /scratch/stefan/7769667/working/building/REAL300000086454 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/474 `/scratch/stefan/7769667/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC(C)C2=CC=C(Br)C=C21)C(=O)[O-]) `REAL300000086454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086454 none CCC(NN=C1CC(C)C2=CC=C(Br)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 14, 14, 14, 14, 14, 9, 5, 1, 1, 1, 2, 2, 2, 1, 1, 1] 14 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 65 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086454 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086454 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086454/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086454 Building REAL300000086455 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086455' /scratch/stefan/7769667/working/building/REAL300000086455 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086455 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086455/0 /scratch/stefan/7769667/working/building/REAL300000086455 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/475 `/scratch/stefan/7769667/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC2=CC(Br)=C(Br)C=C21)C(=O)[O-]) `REAL300000086455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086455 none CCC(NN=C1CCC2=CC(Br)=C(Br)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 1, 1, 1, 17, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 14, 14, 14, 14, 14, 9, 5, 1, 1, 1, 1, 1, 1] 14 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 59 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086455 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086455 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086455/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086455 Building REAL300000086456 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086456' /scratch/stefan/7769667/working/building/REAL300000086456 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086456 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086456/0 /scratch/stefan/7769667/working/building/REAL300000086456 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/476 `/scratch/stefan/7769667/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC(C#N)(C2=CC=CC=N2)CC1)C(=O)[O-]) `REAL300000086456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086456 none CCC(NN=C1CCC(C#N)(C2=CC=CC=N2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [47, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 26, 40, 40, 47, 47, 47, 47, 47, 26, 8, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 1, 1] 93 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 17, 18, 40, 39, 37, 29, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 272 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086456 none CCC(NN=C1CCC(C#N)(C2=CC=CC=N2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 79, 50, 13, 13, 13, 13, 13, 1, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 79, 88, 88, 93, 93, 93, 93, 93, 79, 50, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13] 93 rigid atoms, others: [33, 34, 35, 36, 8, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 394 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086456 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086456 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086456/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086456 Building REAL300000086457 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086457' /scratch/stefan/7769667/working/building/REAL300000086457 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086457 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086457/0 /scratch/stefan/7769667/working/building/REAL300000086457 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/477 `/scratch/stefan/7769667/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC([N+](=O)[O-])=CC(Br)=C1[O-])C(=O)[O-]) `REAL300000086457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086457 none CCC(NN=C(C)C1=CC([N+](=O)[O-])=CC(Br)=C1[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 11, 11, 1, 1, 17, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 25, 25, 26, 26, 26, 26, 26, 20, 13, 4, 4, 4, 1, 1] 26 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086457 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086457 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086457/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086457 Building REAL300000086458 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086458' /scratch/stefan/7769667/working/building/REAL300000086458 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086458 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086458/0 /scratch/stefan/7769667/working/building/REAL300000086458 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/478 `/scratch/stefan/7769667/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CNC2=CC(Br)=CC=C12)C(=O)[O-]) `REAL300000086458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086458 none CCC(NN=CC1=CNC2=CC(Br)=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 1, 17, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 57, 36, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 59, 59, 78, 78, 78, 78, 78, 57, 36, 8, 1, 1, 1, 1, 1] 78 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086458 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086458 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086458/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086458 Building REAL300000086459 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086459' /scratch/stefan/7769667/working/building/REAL300000086459 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086459 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086459/0 /scratch/stefan/7769667/working/building/REAL300000086459 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/479 `/scratch/stefan/7769667/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C)OC(C2=CC=CC(C(F)(F)F)=C2)=N1)C(=O)[O-]) `REAL300000086459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086459 none CCC(NN=CC1=C(C)OC(C2=CC=CC(C(F)(F)F)=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', '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, 5, 8, 8, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 5, 5, 5, 5, 4, 1, 8, 8, 8, 11, 11, 11, 11, 11, 8, 6, 3, 2, 2, 2, 5, 4, 1, 5] 16 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 21] set([0, 1, 2, 3, 4, 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, 38, 39]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086459 none CCC(NN=CC1=C(C)OC(C2=CC=CC(C(F)(F)F)=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', '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, 5, 8, 8, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 13, 8, 8, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 13, 8, 5, 5, 5, 1, 1, 1, 1] 16 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086459 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086459 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086459/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086459 Building REAL300000086460 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086460' /scratch/stefan/7769667/working/building/REAL300000086460 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086460 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086460/0 /scratch/stefan/7769667/working/building/REAL300000086460 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/480 `/scratch/stefan/7769667/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C2CN(C(=O)OC(C)(C)C)CCC2=C1)C(=O)[O-]) `REAL300000086460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086460 none CCC(NN=CC1=CC=C2CN(C(=O)OC(C)(C)C)CCC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 64, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 20, 20, 20, 1, 1, 1, 1, 64, 76, 76, 78, 78, 78, 78, 78, 64, 33, 9, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1] 201 rigid atoms, others: [51, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 47, 48, 49, 50, 19, 20, 21, 22, 37] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 426 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086460 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086460 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086460/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086460 Building REAL300000086461 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086461' /scratch/stefan/7769667/working/building/REAL300000086461 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300000086461 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086461/0 /scratch/stefan/7769667/working/building/REAL300000086461 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/481 `/scratch/stefan/7769667/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC2(CC1)C[N@H+](CC1=CC=CC=C1)CCO2)C(=O)[O-]) `REAL300000086461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086461 none CCC(NN=C1CCC2(CC1)C[N@H+](CC1=CC=CC=C1)CCO2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [19, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 11, 11, 1, 1, 1, 12, 16, 16, 19, 19, 19, 19, 19, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 11, 11, 8, 11, 11, 1, 1, 1, 1] 38 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 51, 52, 53, 54] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 137 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086461 none CCC(NN=C1CCC2(CC1)C[N@H+](CC1=CC=CC=C1)CCO2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 32, 18, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 32, 38, 38, 38, 38, 38, 38, 38, 32, 18, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 1, 11, 11, 11, 11] 38 rigid atoms, others: [48, 49, 50, 46, 15, 16, 17, 18, 19, 20, 14, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 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, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086461 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086461/1 /scratch/stefan/7769667/working/building/REAL300000086461 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/482 `/scratch/stefan/7769667/working/3D/482' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC2(CC1)C[N@@H+](CC1=CC=CC=C1)CCO2)C(=O)[O-]) `REAL300000086461.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086461 none CCC(NN=C1CCC2(CC1)C[N@@H+](CC1=CC=CC=C1)CCO2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [18, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 12, 10, 12, 12, 1, 1, 1, 15, 18, 18, 18, 18, 18, 18, 18, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 12, 12, 10, 12, 12, 1, 1, 1, 1] 45 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 51, 52, 53, 54] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 119 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086461 none CCC(NN=C1CCC2(CC1)C[N@@H+](CC1=CC=CC=C1)CCO2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 40, 27, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 40, 45, 45, 45, 45, 45, 45, 45, 40, 27, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 1, 12, 12, 12, 12] 45 rigid atoms, others: [48, 49, 50, 46, 15, 16, 17, 18, 19, 20, 14, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 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, 51, 52, 53, 54]) total number of confs: 195 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086461 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `2' /scratch/stefan/7769667/working/building/REAL300000086461/2 /scratch/stefan/7769667/working/building/REAL300000086461 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 2 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/483 `/scratch/stefan/7769667/working/3D/483' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC2(CC1)CN(CC1=CC=CC=C1)CCO2)C(=O)[O-]) `REAL300000086461.mol2' -> `2.mol2' `temp.mol2' -> `REAL300000086461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086461/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086461 none CCC(NN=C1CCC2(CC1)CN(CC1=CC=CC=C1)CCO2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [45, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 14, 14, 12, 14, 14, 1, 1, 1, 25, 38, 38, 45, 45, 45, 45, 45, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 14, 14, 12, 14, 14, 1, 1, 1, 1] 94 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52, 53] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 291 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086461 none CCC(NN=C1CCC2(CC1)CN(CC1=CC=CC=C1)CCO2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 85, 52, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 85, 94, 94, 94, 94, 94, 94, 94, 85, 52, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 14, 14, 14, 14] 94 rigid atoms, others: [48, 49, 47, 45, 14, 13, 16, 17, 18, 19, 46, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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, 50, 51, 52, 53]) total number of confs: 387 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086461 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086461 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 2: /scratch/stefan/7769667/working/building/REAL300000086461/2.* 0: /scratch/stefan/7769667/working/building/REAL300000086461/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086461/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086461 Building REAL300000086462 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086462' /scratch/stefan/7769667/working/building/REAL300000086462 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086462 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086462/0 /scratch/stefan/7769667/working/building/REAL300000086462 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/484 `/scratch/stefan/7769667/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C)C=C(Br)C=C1C)C(=O)[O-]) `REAL300000086462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086462 none CCC(NN=CC1=C(C)C=C(Br)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 5, 1, 1, 17, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 35, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 36, 36, 47, 47, 47, 47, 47, 35, 25, 7, 2, 2, 2, 1, 1, 2, 2, 2] 47 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086462 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086462 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086462/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086462 Building REAL300000086463 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086463' /scratch/stefan/7769667/working/building/REAL300000086463 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086463 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086463/0 /scratch/stefan/7769667/working/building/REAL300000086463 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/485 `/scratch/stefan/7769667/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC2(CC2CNC(=O)OC(C)(C)C)CC1)C(=O)[O-]) `REAL300000086463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086463 none CCC(NN=C1CCC2(CC2CNC(=O)OC(C)(C)C)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 28, 47, 47, 71, 73, 73, 73, 1, 1, 18, 26, 26, 27, 27, 27, 27, 27, 18, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 73, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 32, 33, 34, 35, 36, 37, 38, 51, 52, 53, 54] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 349 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086463 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086463 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086463/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086463 Building REAL300000086464 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086464' /scratch/stefan/7769667/working/building/REAL300000086464 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086464 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086464/0 /scratch/stefan/7769667/working/building/REAL300000086464 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/486 `/scratch/stefan/7769667/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(O)C=CC(F)=C1Br)C(=O)[O-]) `REAL300000086464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086464 none CCC(NN=CC1=C(O)C=CC(F)=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 12, 1, 1, 1, 15, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [84, 62, 40, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 65, 65, 84, 84, 84, 84, 84, 62, 40, 12, 2, 1, 1] 168 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 359 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086464 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086464/1 /scratch/stefan/7769667/working/building/REAL300000086464 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/487 `/scratch/stefan/7769667/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C([O-])C=CC(F)=C1Br)C(=O)[O-]) `REAL300000086464.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086464 none CCC(NN=CC1=C([O-])C=CC(F)=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 12, 1, 1, 1, 15, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 21, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 26, 26, 31, 31, 31, 31, 31, 21, 15, 5, 1, 1] 31 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086464 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086464 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086464/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086464/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086464 Building REAL300000086465 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086465' /scratch/stefan/7769667/working/building/REAL300000086465 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086465 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086465/0 /scratch/stefan/7769667/working/building/REAL300000086465 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/488 `/scratch/stefan/7769667/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(OCC(=O)[O-])C(Cl)=C1)C(=O)[O-]) `REAL300000086465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086465 none CCC(NN=CC1=CC=C(OCC(=O)[O-])C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.co2', 'O.co2', '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, 12, 5, 1, 11, 11, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 52, 25, 6, 6, 1, 1, 1, 1, 1, 1, 9, 35, 59, 59, 1, 1, 1, 52, 78, 78, 82, 82, 82, 82, 82, 52, 25, 6, 1, 1, 35, 35, 1] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 15, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 650 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086465 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086465 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086465/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086465 Building REAL300000086466 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086466' /scratch/stefan/7769667/working/building/REAL300000086466 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086466 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086466/0 /scratch/stefan/7769667/working/building/REAL300000086466 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/489 `/scratch/stefan/7769667/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1)C(=O)[O-]) `REAL300000086466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086466 none CCC(NN=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.co2', 'O.co2', '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, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 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: [72, 44, 20, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 37, 53, 53, 1, 1, 44, 66, 66, 72, 72, 72, 72, 72, 44, 20, 5, 1, 1, 9, 37, 37, 1, 1] 201 rigid atoms, others: [32, 36, 5, 6, 7, 8, 9, 10, 18, 19, 37, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 592 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086466 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086466 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086466/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086466 Building REAL300000086467 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086467' /scratch/stefan/7769667/working/building/REAL300000086467 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086467 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086467/0 /scratch/stefan/7769667/working/building/REAL300000086467 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/490 `/scratch/stefan/7769667/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(C)C=C1Br)C(=O)[O-]) `REAL300000086467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086467 none CCC(NN=C(C)C1=CC=C(C)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 5, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 43, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 43, 45, 45, 58, 58, 58, 58, 58, 43, 26, 9, 9, 9, 1, 1, 2, 2, 2, 1] 58 rigid atoms, others: [33, 5, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32]) total number of confs: 247 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086467 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086467 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086467/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086467 Building REAL300000086468 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086468' /scratch/stefan/7769667/working/building/REAL300000086468 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086468 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086468/0 /scratch/stefan/7769667/working/building/REAL300000086468 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/491 `/scratch/stefan/7769667/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CC1CC1)C1=CC=CC(Br)=C1)C(=O)[O-]) `REAL300000086468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086468 none CCC(NN=C(CC1CC1)C1=CC=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 78, 43, 17, 17, 3, 1, 1, 1, 1, 17, 67, 67, 67, 67, 67, 67, 78, 96, 96, 104, 104, 104, 104, 104, 78, 43, 3, 3, 1, 1, 1, 1, 1, 67, 67, 67, 67] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37]) total number of confs: 574 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086468 none CCC(NN=C(CC1CC1)C1=CC=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 119, 62, 13, 13, 1, 13, 47, 67, 67, 1, 1, 1, 1, 1, 1, 1, 119, 151, 151, 166, 166, 166, 166, 166, 119, 62, 47, 47, 67, 67, 67, 67, 67, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 10, 11, 12, 13, 14, 15, 16, 37] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 1050 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086468 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086468 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086468/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086468 Building REAL300000086469 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086469' /scratch/stefan/7769667/working/building/REAL300000086469 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086469 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086469/0 /scratch/stefan/7769667/working/building/REAL300000086469 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/492 `/scratch/stefan/7769667/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC2(CC1)CN(C(=O)OC(C)(C)C)CCO2)C(=O)[O-]) `REAL300000086469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086469 none CCC(NN=C1CCC2(CC1)CN(C(=O)OC(C)(C)C)CCO2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 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, 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: [46, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 24, 24, 24, 1, 1, 1, 26, 41, 41, 46, 46, 46, 46, 46, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1] 107 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 318 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086469 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086469 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086469/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086469 Building REAL300000086470 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086470' /scratch/stefan/7769667/working/building/REAL300000086470 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086470 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086470/0 /scratch/stefan/7769667/working/building/REAL300000086470 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/493 `/scratch/stefan/7769667/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(Br)N=C(C(F)F)S1)C(=O)[O-]) `REAL300000086470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086470 none CCC(NN=CC1=C(Br)N=C(C(F)F)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'F', 'F', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 17, 8, 1, 5, 15, 15, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [126, 88, 51, 10, 10, 1, 1, 1, 1, 1, 1, 1, 12, 12, 1, 88, 110, 110, 126, 126, 126, 126, 126, 88, 50, 10, 12] 183 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 14] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 641 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086470 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086470 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086470/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086470 Building REAL300000086471 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086471' /scratch/stefan/7769667/working/building/REAL300000086471 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086471 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086471/0 /scratch/stefan/7769667/working/building/REAL300000086471 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/494 `/scratch/stefan/7769667/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCCC(CCNC(=O)OC(C)(C)C)C1)C(=O)[O-]) `REAL300000086471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086471 none CCC(NN=C1CCCC(CCNC(=O)OC(C)(C)C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 36, 60, 60, 72, 72, 72, 72, 1, 14, 22, 22, 24, 24, 24, 24, 24, 14, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 36, 72, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35, 20, 53, 36, 52, 37, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 361 number of broken/clashed sets: 123 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086471 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086471 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086471/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086471 Building REAL300000086472 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086472' /scratch/stefan/7769667/working/building/REAL300000086472 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086472 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086472/0 /scratch/stefan/7769667/working/building/REAL300000086472 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/495 `/scratch/stefan/7769667/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C)C=C(Br)S1)C(=O)[O-]) `REAL300000086472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086472 none CCC(NN=CC1=C(C)C=C(Br)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 5, 1, 1, 17, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 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: [77, 56, 42, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 56, 60, 60, 77, 77, 77, 77, 77, 56, 41, 9, 2, 2, 2, 1] 78 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086472 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086472 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086472/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086472 Building REAL300000086473 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086473' /scratch/stefan/7769667/working/building/REAL300000086473 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086473 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086473/0 /scratch/stefan/7769667/working/building/REAL300000086473 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/496 `/scratch/stefan/7769667/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC(CC)C(=O)[O-])C1=CC(Cl)=CC(Cl)=C1) `REAL300000086473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086473 none CCC(=NNC(CC)C(=O)[O-])C1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 5, 5, 1, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 1, 10, 10, 17, 21, 31, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 17, 21, 31, 31, 31, 31, 31, 1, 1, 1] 31 rigid atoms, others: [32, 33, 2, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 136 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086473 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086473 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086473/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086473 Building REAL300000086474 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086474' /scratch/stefan/7769667/working/building/REAL300000086474 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086474 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086474/0 /scratch/stefan/7769667/working/building/REAL300000086474 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/497 `/scratch/stefan/7769667/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC2CCC(C1)[N@@H+]2CC1=CC=CC=C1)C(=O)[O-]) `REAL300000086474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086474 none CCC(NN=C1CCC2CCC(C1)[N@@H+]2CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', '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', '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, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 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, 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: [26, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 6, 8, 8, 19, 24, 24, 26, 26, 26, 26, 26, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8] 52 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086474 none CCC(NN=C1CCC2CCC(C1)[N@@H+]2CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', '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', '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, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 41, 27, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 41, 52, 52, 52, 52, 52, 52, 52, 41, 27, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1] 52 rigid atoms, others: [48, 49, 50, 46, 15, 16, 17, 18, 19, 20, 21, 47] 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, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 259 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086474 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086474/1 /scratch/stefan/7769667/working/building/REAL300000086474 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/498 `/scratch/stefan/7769667/working/3D/498' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC2CCC(C1)[N@H+]2CC1=CC=CC=C1)C(=O)[O-]) `REAL300000086474.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086474 none CCC(NN=C1CCC2CCC(C1)[N@H+]2CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', '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', '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, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [33, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 2, 3, 3, 21, 28, 28, 33, 33, 33, 33, 33, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 2, 3, 3] 34 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086474 none CCC(NN=C1CCC2CCC(C1)[N@H+]2CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', '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', '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, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 27, 34, 34, 34, 34, 34, 34, 34, 27, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 34 rigid atoms, others: [48, 49, 50, 46, 15, 16, 17, 18, 19, 20, 21, 47] 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, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 169 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086474 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086474 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086474/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086474/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086474 Building REAL300000086475 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086475' /scratch/stefan/7769667/working/building/REAL300000086475 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086475 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086475/0 /scratch/stefan/7769667/working/building/REAL300000086475 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/499 `/scratch/stefan/7769667/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C)C=C(S(N)(=O)=O)S1)C(=O)[O-]) `REAL300000086475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086475 none CCC(NN=CC1=C(C)C=C(S(N)(=O)=O)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'S.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, 5, 5, 8, 8, 1, 1, 1, 5, 1, 1, 14, 8, 11, 11, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 2, 2, 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: [76, 49, 25, 10, 10, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 49, 59, 59, 76, 76, 76, 76, 76, 49, 25, 10, 2, 2, 2, 1, 5, 5] 149 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 15, 30] set([0, 1, 2, 3, 4, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086475 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086475 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086475/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086475 Building REAL300000086476 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086476' /scratch/stefan/7769667/working/building/REAL300000086476 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086476 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086476/0 /scratch/stefan/7769667/working/building/REAL300000086476 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/500 `/scratch/stefan/7769667/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=NC2=CC(Cl)=CC=C2N1C(C)C)C(=O)[O-]) `REAL300000086476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086476 none CCC(NN=CC1=NC2=CC(Cl)=CC=C2N1C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.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, 5, 5, 8, 8, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 8, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 23, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 23, 26, 26, 26, 26, 26, 26, 26, 23, 11, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2] 26 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086476 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086476 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086476/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086476 Building REAL300000086477 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086477' /scratch/stefan/7769667/working/building/REAL300000086477 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086477 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086477/0 /scratch/stefan/7769667/working/building/REAL300000086477 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/501 `/scratch/stefan/7769667/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Cl)=CC(Cl)=C1Br)C(=O)[O-]) `REAL300000086477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086477 none CCC(NN=CC1=CC(Cl)=CC(Cl)=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 42, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 45, 45, 56, 56, 56, 56, 56, 42, 30, 9, 1, 1] 56 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086477 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086477 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086477/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086477 Building REAL300000086478 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086478' /scratch/stefan/7769667/working/building/REAL300000086478 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086478 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086478/0 /scratch/stefan/7769667/working/building/REAL300000086478 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/502 `/scratch/stefan/7769667/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)NC1=CC=C(CNN=C(CC)C(=O)[O-])C=C1) `REAL300000086478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086478 none CCCCC(=O)NC1=CC=C(CNN=C(CC)C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens 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, 25, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 18, 30, 30, 59, 30, 35, 35, 1, 1, 29, 29, 29, 29, 29, 29, 29, 19, 19, 3, 1, 1, 4, 4, 18, 59, 59, 59, 59, 59, 1, 1] 201 rigid atoms, others: [32, 33, 43, 6, 7, 8, 9, 10, 11, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086478 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086478 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086478/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086478 Building REAL300000086479 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086479' /scratch/stefan/7769667/working/building/REAL300000086479 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086479 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086479/0 /scratch/stefan/7769667/working/building/REAL300000086479 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/503 `/scratch/stefan/7769667/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC2(C1)CC(COCC1=CC=CC=C1)C2)C(=O)[O-]) `REAL300000086479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086479 none CCC(NN=C1CC2(C1)CC(COCC1=CC=CC=C1)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 69, 119, 119, 69, 119, 119, 1, 12, 17, 17, 18, 18, 18, 18, 18, 12, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 69, 69, 119, 119, 69, 119, 119, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 47, 48, 35, 20, 36, 37, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 524 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086479 none CCC(NN=C1CC2(C1)CC(COCC1=CC=CC=C1)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 147, 119, 119, 119, 119, 119, 119, 119, 54, 14, 4, 1, 1, 1, 1, 1, 1, 1, 119, 198, 201, 201, 201, 201, 201, 201, 201, 198, 147, 119, 119, 119, 119, 119, 119, 119, 54, 54, 4, 4, 1, 1, 1, 1, 1, 119, 119] 201 rigid atoms, others: [45, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48]) total number of confs: 835 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086479 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086479 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086479/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086479 Building REAL300000086480 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086480' /scratch/stefan/7769667/working/building/REAL300000086480 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086480 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086480/0 /scratch/stefan/7769667/working/building/REAL300000086480 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/504 `/scratch/stefan/7769667/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(C(=O)OC)=C1Br)C(=O)[O-]) `REAL300000086480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086480 none CCC(NN=CC1=CC=CC(C(=O)OC)=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'Br', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 2, 2, 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, 14, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 1, 1, 14, 14, 14, 23, 23, 23, 23, 23, 14, 10, 4, 1, 1, 1, 6, 6, 6] 37 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086480 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086480 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086480/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086480 Building REAL300000086481 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086481' /scratch/stefan/7769667/working/building/REAL300000086481 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086481 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086481/0 /scratch/stefan/7769667/working/building/REAL300000086481 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/505 `/scratch/stefan/7769667/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC(C2=CC=C(OC(F)(F)F)C=C2)C1)C(=O)[O-]) `REAL300000086481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086481 none CCC(NN=C1CC(C2=CC=C(OC(F)(F)F)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [9, 6, 4, 1, 1, 1, 1, 1, 1, 4, 4, 1, 2, 19, 23, 23, 23, 4, 4, 1, 6, 6, 6, 9, 9, 9, 9, 9, 6, 4, 1, 1, 1, 4, 4, 4, 4, 1, 1] 43 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 19, 38, 37, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086481 none CCC(NN=C1CC(C2=CC=C(OC(F)(F)F)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [16, 10, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 11, 15, 15, 15, 1, 1, 4, 10, 10, 10, 16, 16, 16, 16, 16, 10, 9, 4, 4, 4, 1, 1, 1, 1, 4, 4] 43 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086481 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086481 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086481/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086481 Building REAL300000086482 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086482' /scratch/stefan/7769667/working/building/REAL300000086482 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086482 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086482/0 /scratch/stefan/7769667/working/building/REAL300000086482 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/506 `/scratch/stefan/7769667/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=C(OC)C=C(Br)C=C1OC)C(=O)[O-]) `REAL300000086482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086482 none CCC(NN=C(C)C1=C(OC)C=C(Br)C=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 12, 5, 1, 1, 17, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 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: [59, 43, 23, 6, 6, 1, 6, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 3, 43, 58, 58, 59, 59, 59, 59, 59, 43, 23, 7, 7, 7, 3, 3, 3, 1, 1, 4, 4, 4] 73 rigid atoms, others: [34, 35, 5, 7, 8, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 6, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 334 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086482 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086482 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086482/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086482 Building REAL300000086483 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086483' /scratch/stefan/7769667/working/building/REAL300000086483 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086483 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086483/0 /scratch/stefan/7769667/working/building/REAL300000086483 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/507 `/scratch/stefan/7769667/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=C(Br)C=C(OC)C=C1OC)C(=O)[O-]) `REAL300000086483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086483 none CCC(NN=C(C)C1=C(Br)C=C(OC)C=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 17, 1, 1, 12, 5, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [96, 70, 31, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 3, 70, 86, 86, 96, 96, 96, 96, 96, 70, 31, 7, 7, 7, 1, 3, 3, 3, 1, 4, 4, 4] 121 rigid atoms, others: [35, 5, 7, 8, 9, 10, 11, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 36, 37, 38]) total number of confs: 489 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086483 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086483 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086483/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086483 Building REAL300000086484 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086484' /scratch/stefan/7769667/working/building/REAL300000086484 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086484 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086484/0 /scratch/stefan/7769667/working/building/REAL300000086484 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/508 `/scratch/stefan/7769667/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC2(CC2)C2=CC(F)=CC(F)=C21)C(=O)[O-]) `REAL300000086484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086484 none CCC(NN=C1CCC2(CC2)C2=CC(F)=CC(F)=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 5, 5, 5, 5, 1, 1, 1, 15, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 17, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 19, 19, 20, 20, 20, 20, 20, 17, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 20 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 88 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086484 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086484 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086484/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086484 Building REAL300000086485 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086485' /scratch/stefan/7769667/working/building/REAL300000086485 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086485 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086485/0 /scratch/stefan/7769667/working/building/REAL300000086485 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/509 `/scratch/stefan/7769667/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CSC(Br)=C1Br)C(=O)[O-]) `REAL300000086485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086485 none CCC(NN=CC1=CSC(Br)=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 14, 1, 17, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [62, 46, 30, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 46, 48, 48, 62, 62, 62, 62, 62, 46, 30, 10, 1] 63 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 24] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086485 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086485 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086485/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086485 Building REAL300000086486 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086486' /scratch/stefan/7769667/working/building/REAL300000086486 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086486 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086486/0 /scratch/stefan/7769667/working/building/REAL300000086486 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/510 `/scratch/stefan/7769667/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(Br)=C1Br)C(=O)[O-]) `REAL300000086486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086486 none CCC(NN=CC1=CC=CC(Br)=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 38, 38, 50, 50, 50, 50, 50, 37, 26, 8, 1, 1, 1] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086486 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086486 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086486/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086486 Building REAL300000086487 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086487' /scratch/stefan/7769667/working/building/REAL300000086487 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086487 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086487/0 /scratch/stefan/7769667/working/building/REAL300000086487 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/511 `/scratch/stefan/7769667/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=NN1[C@H]1C[C@H](C(=O)OC)C1)C(=O)[O-]) `REAL300000086487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086487 none CCC(NN=CC1=CC=NN1[C@H]1C[C@H](C(=O)OC)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [38, 26, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 6, 26, 30, 30, 38, 38, 38, 38, 38, 26, 17, 7, 1, 1, 6, 6, 14, 14, 14, 6, 6] 124 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086487 none CCC(NN=CC1=CC=NN1[C@H]1C[C@H](C(=O)OC)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [76, 56, 47, 26, 26, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 56, 61, 61, 76, 76, 76, 76, 76, 56, 47, 26, 6, 6, 1, 1, 4, 4, 4, 1, 1] 124 rigid atoms, others: [34, 35, 39, 40, 10, 11, 12, 13, 14, 15, 16, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 324 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086487 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086487 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086487/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086487 Building REAL300000086488 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086488' /scratch/stefan/7769667/working/building/REAL300000086488 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086488 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086488/0 /scratch/stefan/7769667/working/building/REAL300000086488 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/512 `/scratch/stefan/7769667/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(C)C(Br)=C(Br)S1)C(=O)[O-]) `REAL300000086488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086488 none CCC(NN=CC1=C(C)C(Br)=C(Br)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'Br', 'C.2', 'Br', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 5, 1, 17, 1, 17, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [83, 61, 42, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 66, 66, 83, 83, 83, 83, 83, 61, 42, 10, 2, 2, 2] 85 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086488 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086488 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086488/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086488 Building REAL300000086489 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086489' /scratch/stefan/7769667/working/building/REAL300000086489 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086489 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086489/0 /scratch/stefan/7769667/working/building/REAL300000086489 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/513 `/scratch/stefan/7769667/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=NN([C@H]2C[C@H](C(=O)OC)C2)C=C1)C(=O)[O-]) `REAL300000086489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086489 none CCC(NN=CC1=NN([C@H]2C[C@H](C(=O)OC)C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 8, 5, 7, 5, 5, 7, 1, 11, 12, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 6, 3, 3, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 8, 1, 1, 9, 9, 9, 14, 14, 14, 14, 14, 9, 6, 3, 8, 8, 19, 19, 19, 8, 8, 1, 1] 43 rigid atoms, others: [5, 6, 7, 8, 9, 39, 40, 19, 20] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086489 none CCC(NN=CC1=NN([C@H]2C[C@H](C(=O)OC)C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 8, 5, 7, 5, 5, 7, 1, 11, 12, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [32, 26, 21, 11, 11, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 8, 8, 26, 26, 26, 32, 32, 32, 32, 32, 26, 21, 11, 1, 1, 4, 4, 4, 1, 1, 8, 8] 43 rigid atoms, others: [32, 33, 37, 38, 8, 9, 10, 11, 12, 13, 14, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39, 40]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086489 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086489 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086489/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086489 Building REAL300000086490 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086490' /scratch/stefan/7769667/working/building/REAL300000086490 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086490 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086490/0 /scratch/stefan/7769667/working/building/REAL300000086490 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/514 `/scratch/stefan/7769667/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Cl)=CN=C1Br)C(=O)[O-]) `REAL300000086490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086490 none CCC(NN=CC1=CC(Cl)=CN=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 8, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 46, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 57, 57, 57, 57, 57, 46, 33, 9, 1, 1] 57 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086490 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086490 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086490/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086490 Building REAL300000086491 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086491' /scratch/stefan/7769667/working/building/REAL300000086491 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086491 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086491/0 /scratch/stefan/7769667/working/building/REAL300000086491 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/515 `/scratch/stefan/7769667/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Cl)=C(Br)C=C1O)C(=O)[O-]) `REAL300000086491.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086491 none CCC(NN=CC1=CC(Cl)=C(Br)C=C1O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 17, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 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, 30, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 40, 40, 40, 40, 40, 30, 21, 7, 1, 1, 2] 80 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28]) total number of confs: 153 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086491 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086491/1 /scratch/stefan/7769667/working/building/REAL300000086491 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/516 `/scratch/stefan/7769667/working/3D/516' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Cl)=C(Br)C=C1[O-])C(=O)[O-]) `REAL300000086491.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086491 none CCC(NN=CC1=CC(Cl)=C(Br)C=C1[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 17, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 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, 18, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 19, 19, 25, 25, 25, 25, 25, 18, 12, 4, 1, 1] 25 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086491 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086491 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086491/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086491/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086491 Building REAL300000086492 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086492' /scratch/stefan/7769667/working/building/REAL300000086492 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086492 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086492/0 /scratch/stefan/7769667/working/building/REAL300000086492 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/517 `/scratch/stefan/7769667/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1(C(=O)OCC)CC2(CC(NN=C(CC)C(=O)[O-])C2)C1) `REAL300000086492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086492 none CCOC(=O)C1(C(=O)OCC)CC2(CC(NN=C(CC)C(=O)[O-])C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 11, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 8, 1, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 9, 1, 1, 1, 1, 1, 7, 13, 13, 29, 13, 22, 22, 1, 1, 14, 14, 14, 14, 14, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 7, 29, 29, 29, 29, 29, 1, 1, 1, 1] 201 rigid atoms, others: [3, 36, 5, 6, 39, 47, 11, 12, 13, 14, 15, 48, 49, 35, 46, 23, 24, 38, 37] set([0, 1, 2, 4, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086492 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086492 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086492/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086492 Building REAL300000086493 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086493' /scratch/stefan/7769667/working/building/REAL300000086493 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086493 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086493/0 /scratch/stefan/7769667/working/building/REAL300000086493 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/518 `/scratch/stefan/7769667/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN(C(C)(C)C)N=C1C(C)(C)C)C(=O)[O-]) `REAL300000086493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086493 none CCC(NN=CC1=CN(C(C)(C)C)N=C1C(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 3, 2, 2, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 2, 4, 4, 4, 6, 6, 6, 6, 6, 4, 3, 2, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2] 6 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086493 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086493 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086493/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086493 Building REAL300000086494 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086494' /scratch/stefan/7769667/working/building/REAL300000086494 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086494 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086494/0 /scratch/stefan/7769667/working/building/REAL300000086494 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/519 `/scratch/stefan/7769667/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCCCC2=C(Br)C=CC=C21)C(=O)[O-]) `REAL300000086494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086494 none CCC(NN=C1CCCCC2=C(Br)C=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 12, 12, 12, 12, 12, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 12 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 45 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086494 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086494 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086494/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086494 Building REAL300000086495 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086495' /scratch/stefan/7769667/working/building/REAL300000086495 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086495 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086495/0 /scratch/stefan/7769667/working/building/REAL300000086495 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/520 `/scratch/stefan/7769667/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC(CC2=CC=CC(Cl)=C2)CC1)C(=O)[O-]) `REAL300000086495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086495 none CCC(NN=C1CCC(CC2=CC=CC(Cl)=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 4, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 1, 1, 6, 7, 7, 9, 9, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 1, 1, 1, 1] 30 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 42, 43, 17, 18, 41, 40, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086495 none CCC(NN=C1CCC(CC2=CC=CC(Cl)=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 22, 17, 9, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 22, 26, 26, 30, 30, 30, 30, 30, 22, 17, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 9, 9, 9, 9] 30 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 141 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086495 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086495 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086495/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086495 Building REAL300000086496 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086496' /scratch/stefan/7769667/working/building/REAL300000086496 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086496 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086496/0 /scratch/stefan/7769667/working/building/REAL300000086496 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/521 `/scratch/stefan/7769667/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(C)C(Br)=C1)C(=O)[O-]) `REAL300000086496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086496 none CCC(NN=C(C)C1=CC=C(C)C(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', '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, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 5, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 60, 37, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 60, 65, 65, 86, 86, 86, 86, 86, 60, 37, 10, 10, 10, 1, 1, 2, 2, 2, 1] 86 rigid atoms, others: [33, 5, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32]) total number of confs: 368 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086496 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086496 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086496/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086496 Building REAL300000086497 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086497' /scratch/stefan/7769667/working/building/REAL300000086497 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086497 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086497/0 /scratch/stefan/7769667/working/building/REAL300000086497 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/522 `/scratch/stefan/7769667/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC2=CC(NC(C)=O)=C(Br)C=C21)C(=O)[O-]) `REAL300000086497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086497 none CCC(NN=C1CCC2=CC(NC(C)=O)=C(Br)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 5, 1, 1, 1, 8, 1, 5, 11, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 13, 13, 13, 15, 15, 15, 15, 15, 13, 6, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1] 34 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 38, 29, 30, 31] set([0, 1, 2, 34, 36, 37, 35, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086497 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086497 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086497/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086497 Building REAL300000086498 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086498' /scratch/stefan/7769667/working/building/REAL300000086498 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086498 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086498/0 /scratch/stefan/7769667/working/building/REAL300000086498 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/523 `/scratch/stefan/7769667/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CN=C2SC(Br)=CN12)C(=O)[O-]) `REAL300000086498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086498 none CCC(NN=CC1=CN=C2SC(Br)=CN12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 14, 1, 17, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 55, 36, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 57, 57, 72, 72, 72, 72, 72, 55, 36, 7, 1, 1] 72 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086498 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086498 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086498/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086498 Building REAL300000086499 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086499' /scratch/stefan/7769667/working/building/REAL300000086499 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086499 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086499/0 /scratch/stefan/7769667/working/building/REAL300000086499 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/524 `/scratch/stefan/7769667/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C2C=C(C(=O)[O-])SC2=CC=C1F)C(=O)[O-]) `REAL300000086499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086499 none CCC(NN=CC1=C2C=C(C(=O)[O-])SC2=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.co2', 'O.co2', '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, 11, 11, 14, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 31, 22, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 32, 32, 34, 34, 34, 34, 34, 31, 22, 9, 1, 1, 1] 34 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086499 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086499 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086499/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086499 Building REAL300000086500 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086500' /scratch/stefan/7769667/working/building/REAL300000086500 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086500 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086500/0 /scratch/stefan/7769667/working/building/REAL300000086500 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/525 `/scratch/stefan/7769667/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(OC(F)(F)F)C(Cl)=C1)C(=O)[O-]) `REAL300000086500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086500 none CCC(NN=CC1=CC=C(OC(F)(F)F)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 5, 15, 15, 15, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 73, 38, 7, 7, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 1, 1, 1, 73, 106, 106, 122, 122, 122, 122, 122, 73, 38, 7, 1, 1, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 719 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086500 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086500 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086500/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086500 Building REAL300000086501 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086501' /scratch/stefan/7769667/working/building/REAL300000086501 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086501 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086501/0 /scratch/stefan/7769667/working/building/REAL300000086501 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/526 `/scratch/stefan/7769667/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(C2CC(F)(F)C2(F)F)=C1)C(=O)[O-]) `REAL300000086501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086501 none CCC(NN=CC1=CC=CC(C2CC(F)(F)C2(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 5, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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] 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: [80, 56, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1, 56, 72, 72, 80, 80, 80, 80, 80, 56, 27, 9, 1, 1, 1, 6, 6, 6, 1] 141 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 19, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 416 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086501 none CCC(NN=CC1=CC=CC(C2CC(F)(F)C2(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 5, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 125, 86, 37, 37, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 125, 141, 141, 141, 141, 141, 141, 141, 125, 86, 37, 6, 6, 6, 1, 1, 1, 6] 141 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37]) total number of confs: 602 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086501 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086501 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086501/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086501 Building REAL300000086502 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086502' /scratch/stefan/7769667/working/building/REAL300000086502 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086502 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086502/0 /scratch/stefan/7769667/working/building/REAL300000086502 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/527 `/scratch/stefan/7769667/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC(O[Si](C)(C)C(C)(C)C)=C1)C(=O)[O-]) `REAL300000086502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086502 none CCC(NN=CC1=CC=CC(O[Si](C)(C)C(C)(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'Si', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 24, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 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: [69, 39, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 20, 20, 20, 1, 39, 56, 56, 69, 69, 69, 69, 69, 39, 15, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1] 178 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 49, 19, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 452 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086502 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086502 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086502/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086502 Building REAL300000086503 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086503' /scratch/stefan/7769667/working/building/REAL300000086503 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086503 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086503/0 /scratch/stefan/7769667/working/building/REAL300000086503 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/528 `/scratch/stefan/7769667/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(C(=O)OC)=CC(C(F)(F)F)=C1)C(=O)[O-]) `REAL300000086503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086503 none CCC(NN=CC1=CC(C(=O)OC)=CC(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 5, 3, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [18, 12, 11, 7, 7, 1, 1, 1, 1, 1, 6, 6, 6, 1, 1, 1, 2, 2, 2, 1, 12, 12, 12, 18, 18, 18, 18, 18, 12, 11, 7, 1, 7, 7, 7, 1, 1] 27 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 13, 14, 15, 19, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086503 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086503 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086503/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086503 Building REAL300000086504 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086504' /scratch/stefan/7769667/working/building/REAL300000086504 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086504 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086504/0 /scratch/stefan/7769667/working/building/REAL300000086504 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/529 `/scratch/stefan/7769667/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(C(F)(F)F)C(Cl)=C1)C(=O)[O-]) `REAL300000086504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086504 none CCC(NN=C(C)C1=CC=C(C(F)(F)F)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 15, 15, 15, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 74, 45, 11, 11, 1, 11, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 74, 77, 77, 87, 87, 87, 87, 87, 74, 45, 11, 11, 11, 1, 1, 1] 87 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 360 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086504 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086504 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086504/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086504 Building REAL300000086505 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086505' /scratch/stefan/7769667/working/building/REAL300000086505 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086505 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086505/0 /scratch/stefan/7769667/working/building/REAL300000086505 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/530 `/scratch/stefan/7769667/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(C(F)(F)F)C=C1Br)C(=O)[O-]) `REAL300000086505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086505 none CCC(NN=CC1=CC=C(C(F)(F)F)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', '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, 5, 15, 15, 15, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 38, 22, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 38, 38, 38, 45, 45, 45, 45, 45, 38, 22, 8, 1, 1, 1] 45 rigid atoms, others: [5, 6, 7, 8, 9, 10, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086505 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086505 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086505/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086505 Building REAL300000086506 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086506' /scratch/stefan/7769667/working/building/REAL300000086506 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086506 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086506/0 /scratch/stefan/7769667/working/building/REAL300000086506 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/531 `/scratch/stefan/7769667/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC2=NC=C(Br)C=C2O1)C(=O)[O-]) `REAL300000086506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086506 none CCC(NN=CC1=CC2=NC=C(Br)C=C2O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 41, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 43, 43, 57, 57, 57, 57, 57, 41, 25, 7, 1, 1, 1] 57 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086506 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086506 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086506/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086506 Building REAL300000086507 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086507' /scratch/stefan/7769667/working/building/REAL300000086507 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086507 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086507/0 /scratch/stefan/7769667/working/building/REAL300000086507 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/532 `/scratch/stefan/7769667/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC(C(C)(C)C)=CC2=C1CCC2(C)C)C(=O)[O-]) `REAL300000086507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086507 none CCC(NN=C(C)C1=CC(C(C)(C)C)=CC2=C1CCC2(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', '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, 5, 5, 5, 5, 1, 1, 1, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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, 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: [122, 77, 43, 9, 9, 1, 9, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 77, 102, 102, 122, 122, 122, 122, 121, 77, 43, 9, 9, 9, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 136 rigid atoms, others: [48, 35, 5, 7, 8, 9, 10, 45, 14, 15, 16, 17, 18, 19, 20, 46, 49, 47, 21] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52, 53, 54, 55]) total number of confs: 665 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086507 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086507 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086507/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086507 Building REAL300000086508 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086508' /scratch/stefan/7769667/working/building/REAL300000086508 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086508 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086508/0 /scratch/stefan/7769667/working/building/REAL300000086508 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/533 `/scratch/stefan/7769667/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(CC(C)C)C1=CC(C)=CC(Br)=C1)C(=O)[O-]) `REAL300000086508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086508 none CCC(NN=C(CC(C)C)C1=CC(C)=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 5, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 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: [126, 100, 53, 12, 12, 1, 12, 32, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 100, 116, 116, 126, 126, 126, 126, 126, 100, 53, 32, 32, 36, 36, 36, 36, 36, 36, 36, 1, 2, 2, 2, 1, 1] 141 rigid atoms, others: [5, 41, 10, 11, 12, 13, 14, 15, 16, 17, 42, 37] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 18, 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: 699 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086508 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086508 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086508/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086508 Building REAL300000086509 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086509' /scratch/stefan/7769667/working/building/REAL300000086509 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086509 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086509/0 /scratch/stefan/7769667/working/building/REAL300000086509 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/534 `/scratch/stefan/7769667/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC2(CC2(F)F)C2=CC=CC=C21)C(=O)[O-]) `REAL300000086509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086509 none CCC(NN=C1CCC2(CC2(F)F)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 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, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 17, 17, 19, 19, 19, 19, 19, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 19 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 85 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086509 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086509 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086509/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086509 Building REAL300000086510 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086510' /scratch/stefan/7769667/working/building/REAL300000086510 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086510 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086510/0 /scratch/stefan/7769667/working/building/REAL300000086510 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/535 `/scratch/stefan/7769667/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C2SC(C(F)F)=NC2=CC=C1)C(=O)[O-]) `REAL300000086510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086510 none CCC(NN=CC1=C2SC(C(F)F)=NC2=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'F', 'F', 'N.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 14, 1, 5, 15, 15, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 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: [92, 70, 39, 13, 13, 1, 1, 1, 1, 1, 1, 12, 12, 1, 1, 1, 1, 1, 70, 82, 82, 92, 92, 92, 92, 92, 70, 39, 13, 12, 1, 1, 1] 134 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 458 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086510 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086510 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086510/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086510 Building REAL300000086511 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086511' /scratch/stefan/7769667/working/building/REAL300000086511 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086511 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086511/0 /scratch/stefan/7769667/working/building/REAL300000086511 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/536 `/scratch/stefan/7769667/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CN(C(=O)OC(C)(C)C)C2(C1)CCCCC2)C(=O)[O-]) `REAL300000086511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086511 none CCC(NN=C1CN(C(=O)OC(C)(C)C)C2(C1)CCCCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [27, 20, 7, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 20, 25, 25, 27, 27, 27, 27, 27, 20, 7, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 34 rigid atoms, others: [3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086511 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086511 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086511/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086511 Building REAL300000086512 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086512' /scratch/stefan/7769667/working/building/REAL300000086512 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086512 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086512/0 /scratch/stefan/7769667/working/building/REAL300000086512 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/537 `/scratch/stefan/7769667/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CN(C(=O)OC(C)(C)C)C2(CCOC2)C1)C(=O)[O-]) `REAL300000086512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086512 none CCC(NN=C1CN(C(=O)OC(C)(C)C)C2(CCOC2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [43, 27, 7, 1, 1, 1, 1, 1, 1, 6, 6, 13, 15, 15, 15, 1, 1, 1, 1, 1, 1, 27, 37, 37, 43, 43, 43, 43, 43, 27, 7, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1] 73 rigid atoms, others: [3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086512 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086512 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086512/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086512 Building REAL300000086513 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086513' /scratch/stefan/7769667/working/building/REAL300000086513 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086513 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086513/0 /scratch/stefan/7769667/working/building/REAL300000086513 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/538 `/scratch/stefan/7769667/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC2=C(OC)C=C(OC)C=C2N1)C(=O)[O-]) `REAL300000086513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086513 none CCC(NN=CC1=CC2=C(OC)C=C(OC)C=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 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 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [67, 49, 27, 6, 6, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 2, 1, 1, 1, 49, 62, 62, 67, 67, 67, 67, 67, 49, 27, 6, 1, 4, 4, 4, 1, 2, 2, 2, 1, 1] 101 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 39, 12, 13, 14, 16, 17, 18, 38, 30] set([0, 1, 2, 3, 4, 11, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35, 36, 37]) total number of confs: 339 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086513 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086513 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086513/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086513 Building REAL300000086514 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086514' /scratch/stefan/7769667/working/building/REAL300000086514 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086514 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086514/0 /scratch/stefan/7769667/working/building/REAL300000086514 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/539 `/scratch/stefan/7769667/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CNC2=CC(C(F)(F)F)=CC=C12)C(=O)[O-]) `REAL300000086514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086514 none CCC(NN=CC1=CNC2=CC(C(F)(F)F)=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 63, 38, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 63, 65, 65, 69, 69, 69, 69, 69, 63, 38, 9, 1, 1, 1, 1, 1] 69 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086514 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086514 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086514/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086514 Building REAL300000086515 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086515' /scratch/stefan/7769667/working/building/REAL300000086515 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086515 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086515/0 /scratch/stefan/7769667/working/building/REAL300000086515 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/540 `/scratch/stefan/7769667/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC2=CC(Br)=CC=C2S1)C(=O)[O-]) `REAL300000086515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086515 none CCC(NN=CC1=CC2=CC(Br)=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 47, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 49, 49, 64, 64, 64, 64, 64, 47, 30, 7, 1, 1, 1, 1] 64 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 267 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086515 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086515 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086515/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086515 Building REAL300000086516 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086516' /scratch/stefan/7769667/working/building/REAL300000086516 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086516 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086516/0 /scratch/stefan/7769667/working/building/REAL300000086516 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/541 `/scratch/stefan/7769667/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CN(C(=O)OC(C)(C)C)C2(CCCC2)C1)C(=O)[O-]) `REAL300000086516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086516 none CCC(NN=C1CN(C(=O)OC(C)(C)C)C2(CCCC2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [37, 24, 8, 1, 1, 1, 1, 1, 1, 5, 5, 13, 15, 16, 15, 1, 1, 1, 1, 1, 1, 24, 34, 34, 37, 37, 37, 37, 37, 24, 8, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 69 rigid atoms, others: [3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086516 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086516 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086516/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086516 Building REAL300000086517 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086517' /scratch/stefan/7769667/working/building/REAL300000086517 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086517 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086517/0 /scratch/stefan/7769667/working/building/REAL300000086517 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/542 `/scratch/stefan/7769667/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=NC=C(CC2=CC=CC=C2)N1C)C(=O)[O-]) `REAL300000086517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086517 none CCC(NN=CC1=NC=C(CC2=CC=CC=C2)N1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 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: [19, 13, 7, 4, 4, 1, 1, 1, 1, 1, 1, 6, 13, 13, 6, 13, 13, 1, 1, 13, 15, 15, 19, 19, 19, 19, 19, 13, 7, 4, 1, 6, 6, 13, 13, 9, 13, 13, 2, 2, 2] 52 rigid atoms, others: [5, 6, 7, 8, 9, 10, 17, 18, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086517 none CCC(NN=CC1=NC=C(CC2=CC=CC=C2)N1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 47, 32, 20, 20, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 47, 50, 50, 52, 52, 52, 52, 52, 47, 32, 20, 13, 4, 4, 1, 1, 1, 1, 1, 13, 13, 13] 52 rigid atoms, others: [33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086517 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086517 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086517/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086517 Building REAL300000086518 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086518' /scratch/stefan/7769667/working/building/REAL300000086518 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086518 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086518/0 /scratch/stefan/7769667/working/building/REAL300000086518 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/543 `/scratch/stefan/7769667/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(C2=CC=CC(CO)=C2)S1)C(=O)[O-]) `REAL300000086518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086518 none CCC(NN=C(C)C1=CC=C(C2=CC=CC(CO)=C2)S1)C(=O)[O-] 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'S.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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [44, 26, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 66, 12, 1, 26, 32, 32, 44, 44, 44, 44, 44, 26, 14, 7, 7, 7, 1, 1, 12, 12, 12, 66, 66, 198, 12] 603 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 19] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 666 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086518 none CCC(NN=C(C)C1=CC=C(C2=CC=CC(CO)=C2)S1)C(=O)[O-] 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'S.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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [164, 123, 104, 54, 54, 12, 54, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 123, 145, 145, 164, 164, 164, 164, 164, 123, 104, 54, 54, 54, 12, 12, 1, 1, 1, 8, 8, 24, 1] 603 rigid atoms, others: [35, 36, 37, 41, 10, 11, 12, 13, 14, 15, 16, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 774 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086518 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086518 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086518/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086518 Building REAL300000086519 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086519' /scratch/stefan/7769667/working/building/REAL300000086519 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086519 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086519/0 /scratch/stefan/7769667/working/building/REAL300000086519 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/544 `/scratch/stefan/7769667/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(Br)C=C1Br)C(=O)[O-]) `REAL300000086519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086519 none CCC(NN=CC1=CC=C(Br)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 34, 22, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 35, 35, 46, 46, 46, 46, 46, 34, 22, 8, 1, 1, 1] 46 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086519 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086519 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086519/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086519 Building REAL300000086520 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086520' /scratch/stefan/7769667/working/building/REAL300000086520 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086520 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086520/0 /scratch/stefan/7769667/working/building/REAL300000086520 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/545 `/scratch/stefan/7769667/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=CC(F)=C1F)C(=O)[O-]) `REAL300000086520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086520 none CCC(NN=CC1=CC(Br)=CC(F)=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 36, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 37, 37, 47, 47, 47, 47, 47, 36, 26, 8, 1, 1] 47 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086520 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086520 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086520/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086520 Building REAL300000086521 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086521' /scratch/stefan/7769667/working/building/REAL300000086521 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086521 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086521/0 /scratch/stefan/7769667/working/building/REAL300000086521 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/546 `/scratch/stefan/7769667/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC(C2=CC=C(Br)C=C2)C1(C)C)C(=O)[O-]) `REAL300000086521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086521 none CCC(NN=C1CC(C2=CC=C(Br)C=C2)C1(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 2, 1, 1, 1, 19, 22, 22, 23, 23, 23, 23, 23, 19, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 23 rigid atoms, others: [3, 4, 5, 6, 7, 8, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086521 none CCC(NN=C1CC(C2=CC=C(Br)C=C2)C1(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 9, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 22, 22, 23, 23, 23, 23, 23, 19, 9, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 23 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40]) total number of confs: 105 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086521 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086521 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086521/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086521 Building REAL300000086522 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086522' /scratch/stefan/7769667/working/building/REAL300000086522 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086522 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086522/0 /scratch/stefan/7769667/working/building/REAL300000086522 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/547 `/scratch/stefan/7769667/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Cl)=C(Br)C=C1F)C(=O)[O-]) `REAL300000086522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086522 none CCC(NN=CC1=CC(Cl)=C(Br)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 17, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 39, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 40, 40, 52, 52, 52, 52, 52, 39, 25, 8, 1, 1] 52 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086522 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086522 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086522/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086522 Building REAL300000086523 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086523' /scratch/stefan/7769667/working/building/REAL300000086523 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086523 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086523/0 /scratch/stefan/7769667/working/building/REAL300000086523 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/548 `/scratch/stefan/7769667/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=CC([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300000086523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086523 none CCC(NN=CC1=CC(Br)=CC([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 61, 40, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 64, 64, 82, 82, 82, 82, 82, 61, 40, 8, 1, 1, 1] 82 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086523 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086523 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086523/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086523 Building REAL300000086524 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086524' /scratch/stefan/7769667/working/building/REAL300000086524 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086524 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086524/0 /scratch/stefan/7769667/working/building/REAL300000086524 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/549 `/scratch/stefan/7769667/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(Br)C(F)=C1OC)C(=O)[O-]) `REAL300000086524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086524 none CCC(NN=CC1=CC=C(Br)C(F)=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 17, 1, 15, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 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: [47, 34, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 34, 39, 39, 47, 47, 47, 47, 47, 34, 20, 5, 1, 1, 5, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 215 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086524 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086524 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086524/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086524 Building REAL300000086525 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086525' /scratch/stefan/7769667/working/building/REAL300000086525 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086525 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086525/0 /scratch/stefan/7769667/working/building/REAL300000086525 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/550 `/scratch/stefan/7769667/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC2=CC=CC=C2C(Br)=C1)C(=O)[O-]) `REAL300000086525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086525 none CCC(NN=CC1=CC2=CC=CC=C2C(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 55, 34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 58, 58, 73, 73, 73, 73, 73, 55, 34, 9, 1, 1, 1, 1, 1, 1] 73 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086525 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086525 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086525/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086525 Building REAL300000086526 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086526' /scratch/stefan/7769667/working/building/REAL300000086526 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086526 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086526/0 /scratch/stefan/7769667/working/building/REAL300000086526 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/551 `/scratch/stefan/7769667/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=C(CN2C=C(Br)C=N2)C=C1)C(=O)[O-]) `REAL300000086526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086526 none CCC(NN=CC1=CC=C(CN2C=C(Br)C=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 5, 8, 1, 1, 17, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens 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, 42, 22, 4, 4, 1, 1, 1, 1, 1, 1, 6, 33, 33, 33, 33, 33, 1, 1, 42, 62, 62, 68, 68, 68, 68, 68, 42, 22, 4, 1, 1, 6, 6, 33, 33, 1, 1] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 17, 18, 37, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 416 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086526 none CCC(NN=CC1=CC=C(CN2C=C(Br)C=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'C.ar', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 5, 8, 1, 1, 17, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 182, 130, 66, 66, 33, 33, 33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 33, 33, 182, 187, 187, 201, 201, 201, 201, 201, 182, 130, 66, 33, 33, 9, 9, 1, 1, 33, 33] 201 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 801 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086526 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086526 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086526/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086526 Building REAL300000086527 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086527' /scratch/stefan/7769667/working/building/REAL300000086527 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086527 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086527/0 /scratch/stefan/7769667/working/building/REAL300000086527 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/552 `/scratch/stefan/7769667/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(F)C=C(I)C=C1F)C(=O)[O-]) `REAL300000086527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086527 none CCC(NN=CC1=C(F)C=C(I)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 15, 1, 1, 18, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 32, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 33, 33, 44, 44, 44, 44, 44, 32, 26, 7, 1, 1] 44 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086527 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086527 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086527/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086527 Building REAL300000086528 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086528' /scratch/stefan/7769667/working/building/REAL300000086528 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086528 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086528/0 /scratch/stefan/7769667/working/building/REAL300000086528 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/553 `/scratch/stefan/7769667/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1C(=O)N1CCCCC1)C(=O)[O-]) `REAL300000086528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086528 none CCC(NN=CC1=CC=CC=C1C(=O)N1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [44, 34, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 34, 41, 41, 44, 44, 44, 44, 44, 34, 13, 5, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 71 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, 43, 44]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086528 none CCC(NN=CC1=CC=CC=C1C(=O)N1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 65, 38, 20, 20, 9, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 71, 71, 71, 71, 71, 71, 71, 65, 38, 20, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 71 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086528 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086528 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086528/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086528 Building REAL300000086529 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086529' /scratch/stefan/7769667/working/building/REAL300000086529 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086529 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086529/0 /scratch/stefan/7769667/working/building/REAL300000086529 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/554 `/scratch/stefan/7769667/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC=CC=C1OCC1=CC=CC=C1F)C(=O)[O-]) `REAL300000086529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086529 none CCC(NN=CC1=CC=CC=C1OCC1=CC=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'F', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 17, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 32, 105, 105, 52, 105, 105, 105, 17, 27, 27, 31, 31, 31, 31, 31, 17, 7, 4, 1, 1, 1, 1, 32, 32, 105, 105, 105, 105] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12] 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, 36, 37, 38, 39, 40, 41]) total number of confs: 553 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086529 none CCC(NN=CC1=CC=CC=C1OCC1=CC=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'F', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 149, 137, 121, 121, 105, 105, 105, 105, 105, 105, 48, 8, 1, 1, 1, 1, 1, 1, 1, 1, 149, 201, 201, 201, 201, 201, 201, 201, 149, 137, 121, 105, 105, 105, 105, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 869 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086529 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086529 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086529/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086529 Building REAL300000086530 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086530' /scratch/stefan/7769667/working/building/REAL300000086530 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086530 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086530/0 /scratch/stefan/7769667/working/building/REAL300000086530 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/555 `/scratch/stefan/7769667/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC2(CCC3=CC=CC=C32)CC1)C(=O)[O-]) `REAL300000086530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086530 none CCC(NN=C1CCC2(CCC3=CC=CC=C32)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 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, 4, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 18, 18, 18, 18, 18, 18, 18, 14, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 18 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 84 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086530 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086530 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086530/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086530 Building REAL300000086531 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086531' /scratch/stefan/7769667/working/building/REAL300000086531 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086531 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086531/0 /scratch/stefan/7769667/working/building/REAL300000086531 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/556 `/scratch/stefan/7769667/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC(C2=CC=C(Cl)C(Cl)=C2)C2=CC=CC=C21)C(=O)[O-]) `REAL300000086531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086531 none CCC(NN=C1CCC(C2=CC=C(Cl)C(Cl)=C2)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [28, 21, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 4, 6, 7, 7, 7, 1, 1, 1, 1, 1, 1, 21, 26, 26, 28, 28, 28, 28, 28, 21, 7, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1, 1, 1] 45 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 41, 42, 43, 44] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 152 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086531 none CCC(NN=C1CCC(C2=CC=C(Cl)C(Cl)=C2)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 38, 23, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 38, 45, 45, 45, 45, 45, 45, 45, 38, 23, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7] 45 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44]) total number of confs: 201 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086531 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086531 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086531/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086531 Building REAL300000086532 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086532' /scratch/stefan/7769667/working/building/REAL300000086532 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086532 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086532/0 /scratch/stefan/7769667/working/building/REAL300000086532 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/557 `/scratch/stefan/7769667/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC(F)(F)CC1OCC1=CC=CC=C1)C(=O)[O-]) `REAL300000086532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086532 none CCC(NN=C1CCC(F)(F)CC1OCC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 15, 15, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [38, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 38, 38, 21, 38, 38, 21, 34, 34, 38, 38, 38, 38, 38, 21, 7, 1, 1, 1, 1, 1, 1, 1, 19, 19, 38, 38, 38, 38, 38] 179 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35, 36, 37, 31] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 367 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086532 none CCC(NN=C1CCC(F)(F)CC1OCC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 15, 15, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 160, 122, 38, 38, 38, 38, 38, 38, 38, 38, 38, 17, 3, 1, 1, 1, 1, 1, 1, 1, 160, 179, 179, 179, 179, 179, 179, 179, 160, 122, 38, 38, 38, 38, 38, 38, 38, 3, 3, 1, 1, 1, 1, 1] 179 rigid atoms, others: [40, 41, 42, 43, 44, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 734 number of broken/clashed sets: 94 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086532 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086532 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086532/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086532 Building REAL300000086533 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086533' /scratch/stefan/7769667/working/building/REAL300000086533 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086533 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086533/0 /scratch/stefan/7769667/working/building/REAL300000086533 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/558 `/scratch/stefan/7769667/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=C(Br)C=CC(OC)=C1O)C(=O)[O-]) `REAL300000086533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086533 none CCC(NN=CC1=C(Br)C=CC(OC)=C1O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.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, 5, 5, 8, 8, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [18, 12, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 12, 13, 13, 18, 18, 18, 18, 18, 12, 7, 3, 1, 1, 4, 4, 4, 2] 42 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 27, 28] set([0, 1, 2, 3, 4, 32, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 94 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086533 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086533 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086533/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086533 Building REAL300000086534 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086534' /scratch/stefan/7769667/working/building/REAL300000086534 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086534 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086534/0 /scratch/stefan/7769667/working/building/REAL300000086534 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/559 `/scratch/stefan/7769667/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CC(COCC2=CC=CC=C2)C12CCC2)C(=O)[O-]) `REAL300000086534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086534 none CCC(NN=C1CC(COCC2=CC=CC=C2)C12CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 1, 1, 1, 1, 1, 1, 5, 18, 59, 102, 102, 70, 102, 102, 1, 1, 1, 1, 15, 23, 23, 25, 25, 25, 25, 25, 15, 6, 1, 1, 1, 5, 5, 59, 59, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 544 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086534 none CCC(NN=C1CC(COCC2=CC=CC=C2)C12CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 156, 102, 102, 102, 102, 56, 15, 3, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 198, 201, 201, 201, 201, 201, 201, 201, 198, 156, 102, 102, 102, 56, 56, 3, 3, 1, 1, 1, 1, 1, 102, 102, 102, 102, 102, 102] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48]) total number of confs: 815 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086534 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086534 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086534/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086534 Building REAL300000086535 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086535' /scratch/stefan/7769667/working/building/REAL300000086535 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086535 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086535/0 /scratch/stefan/7769667/working/building/REAL300000086535 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/560 `/scratch/stefan/7769667/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=CC1=CC(Br)=CC(C(=O)OC)=C1)C(=O)[O-]) `REAL300000086535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086535 none CCC(NN=CC1=CC(Br)=CC(C(=O)OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', '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, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [86, 52, 28, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 1, 52, 69, 69, 86, 86, 86, 86, 86, 52, 28, 9, 1, 1, 10, 10, 10, 1] 146 rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 11, 12, 16, 28, 29] set([0, 1, 2, 3, 4, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32]) total number of confs: 460 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086535 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086535 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086535/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086535 Building REAL300000086536 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086536' /scratch/stefan/7769667/working/building/REAL300000086536 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086536 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086536/0 /scratch/stefan/7769667/working/building/REAL300000086536 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/561 `/scratch/stefan/7769667/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C1CCC(C2CCN(C(=O)OC(C)(C)C)CC2)CC1)C(=O)[O-]) `REAL300000086536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086536 none CCC(NN=C1CCC(C2CCN(C(=O)OC(C)(C)C)CC2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 7, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 29, 29, 62, 69, 69, 69, 8, 8, 1, 1, 20, 31, 31, 34, 34, 34, 34, 34, 20, 7, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 69, 69, 69, 69, 69, 69, 69, 69, 69, 8, 8, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 59, 35, 57, 22, 23, 36, 58, 38, 60, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 351 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086536 none CCC(NN=C1CCC(C2CCN(C(=O)OC(C)(C)C)CC2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 70, 40, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 6, 6, 14, 16, 16, 16, 1, 1, 8, 8, 70, 85, 85, 93, 93, 93, 93, 93, 70, 40, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 8, 8, 8, 8] 201 rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 40, 20, 21, 54, 41, 56, 55, 42, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51, 52, 57, 58, 59, 60]) total number of confs: 480 number of broken/clashed sets: 128 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086536 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086536 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086536/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086536 Building REAL300000086537 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086537' /scratch/stefan/7769667/working/building/REAL300000086537 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086537 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086537/0 /scratch/stefan/7769667/working/building/REAL300000086537 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/562 `/scratch/stefan/7769667/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)CC1=CC=CC(F)=C1Br)C(=O)[O-]) `REAL300000086537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086537 none CCC(NN=C(C)CC1=CC=CC(F)=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', '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, 5, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 15, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 108, 67, 24, 24, 6, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 122, 122, 151, 151, 151, 151, 151, 108, 67, 24, 24, 24, 6, 6, 1, 1, 1] 151 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 715 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086537 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086537 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086537/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086537 Building REAL300000086538 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086538' /scratch/stefan/7769667/working/building/REAL300000086538 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086538 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086538/0 /scratch/stefan/7769667/working/building/REAL300000086538 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/563 `/scratch/stefan/7769667/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NN=C(C)C1=CC=C(C(F)(F)F)C=C1F)C(=O)[O-]) `REAL300000086538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086538 none CCC(NN=C(C)C1=CC=C(C(F)(F)F)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 5, 15, 15, 15, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 55, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 55, 59, 59, 69, 69, 69, 69, 69, 55, 37, 11, 11, 11, 1, 1, 1] 69 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 295 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086538 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086538 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086538/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086538 Building REAL300000086539 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086539' /scratch/stefan/7769667/working/building/REAL300000086539 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086539 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086539/0 /scratch/stefan/7769667/working/building/REAL300000086539 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/564 `/scratch/stefan/7769667/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)N2CCC(C(=O)[O-])CC2)C=C1) `REAL300000086539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086539 none CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)N2CCC(C(=O)[O-])CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 5, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 30, 7, 3, 1, 1, 1, 1, 48, 101, 101, 74, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 101, 48, 48, 48, 7, 7, 3, 3, 1, 1, 1, 1, 1, 101, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 101] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 38, 37] set([0, 1, 2, 3, 4, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 730 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086539 none CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)N2CCC(C(=O)[O-])CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 5, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 28, 28, 42, 105, 165, 201, 201, 6, 11, 11, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 1, 1, 11, 11, 28, 28, 28, 105, 105, 165, 165, 201, 201, 201, 201, 201, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 201 rigid atoms, others: [48, 49, 41, 42, 43, 44, 13, 46, 45, 16, 17, 18, 19, 20, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 861 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086539 none CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)N2CCC(C(=O)[O-])CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 5, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 46, 75, 101, 101, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 11, 19, 19, 11, 11, 1, 1, 6, 6, 6, 46, 46, 75, 75, 101, 101, 101, 101, 101, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1] 201 rigid atoms, others: [1, 39, 40, 9, 10, 11, 12, 13, 50, 51, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 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: 470 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086539 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086539 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086539/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086539 Building REAL300000086540 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086540' /scratch/stefan/7769667/working/building/REAL300000086540 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086540 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086540/0 /scratch/stefan/7769667/working/building/REAL300000086540 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/565 `/scratch/stefan/7769667/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1) `REAL300000086540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086540 none CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 3, 1, 1, 1, 1, 19, 35, 35, 35, 35, 127, 127, 127, 178, 178, 193, 193, 201, 201, 201, 35, 35, 19, 19, 19, 7, 7, 3, 3, 1, 1, 1, 1, 1, 35, 35, 178, 178, 178, 193, 193, 193, 193, 201, 201, 35, 35] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 37] set([0, 1, 2, 3, 4, 9, 10, 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, 49, 50]) total number of confs: 775 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086540 none CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 3, 11, 21, 35, 35, 1, 1, 1, 1, 1, 8, 8, 8, 16, 16, 35, 35, 39, 52, 52, 1, 1, 3, 3, 3, 11, 11, 21, 21, 35, 35, 35, 35, 35, 1, 1, 17, 17, 17, 35, 35, 35, 35, 39, 39, 1, 1] 201 rigid atoms, others: [1, 38, 39, 9, 10, 11, 12, 13, 49, 50, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 365 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086540 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086540 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086540/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086540 Building REAL300000086541 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086541' /scratch/stefan/7769667/working/building/REAL300000086541 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086541 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086541/0 /scratch/stefan/7769667/working/building/REAL300000086541 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/566 `/scratch/stefan/7769667/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NOCCC1CC1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1) `REAL300000086541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086541 none CC(=NOCCC1CC1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 35, 7, 3, 1, 1, 1, 1, 78, 121, 121, 78, 78, 199, 199, 199, 199, 199, 199, 199, 121, 121, 78, 78, 78, 7, 7, 3, 3, 1, 1, 1, 1, 1, 121, 121, 199, 199, 121, 121] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 3, 4, 9, 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]) total number of confs: 482 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086541 none CC(=NOCCC1CC1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 12, 12, 31, 94, 147, 199, 199, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 13, 13, 94, 94, 148, 147, 199, 199, 199, 199, 199, 12, 12, 1, 1, 12, 12] 201 rigid atoms, others: [37, 38, 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, 39, 40]) total number of confs: 837 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086541 none CC(=NOCCC1CC1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 55, 90, 121, 121, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 6, 6, 6, 55, 55, 90, 90, 121, 121, 121, 121, 121, 1, 1, 12, 12, 1, 1] 201 rigid atoms, others: [1, 35, 36, 39, 40, 9, 10, 11, 12, 13, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 504 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086541 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086541 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086541/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086541 Building REAL300000086542 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086542' /scratch/stefan/7769667/working/building/REAL300000086542 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086542 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086542/0 /scratch/stefan/7769667/working/building/REAL300000086542 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/567 `/scratch/stefan/7769667/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)N2CCCCC2C(=O)[O-])C=C1) `REAL300000086542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086542 none CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)N2CCCCC2C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 96, 42, 7, 3, 1, 1, 1, 1, 96, 163, 163, 143, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 163, 96, 96, 96, 7, 7, 3, 3, 1, 1, 1, 1, 1, 163, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 163] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 38, 37] set([0, 1, 2, 3, 4, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 569 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086542 none CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)N2CCCCC2C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 16, 16, 66, 148, 191, 201, 201, 2, 4, 4, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 16, 16, 16, 148, 148, 191, 191, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 201 rigid atoms, others: [48, 49, 41, 42, 43, 44, 13, 46, 45, 16, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 728 number of broken/clashed sets: 35 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086542 none CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)N2CCCCC2C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 31, 105, 146, 163, 163, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 6, 6, 6, 105, 105, 146, 146, 163, 163, 163, 163, 163, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 201 rigid atoms, others: [1, 39, 40, 9, 10, 11, 12, 13, 50, 51, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 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: 630 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086542 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086542 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086542/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086542 Building REAL300000086543 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086543' /scratch/stefan/7769667/working/building/REAL300000086543 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086543 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086543/0 /scratch/stefan/7769667/working/building/REAL300000086543 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/568 `/scratch/stefan/7769667/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1) `REAL300000086543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086543 none CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', '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, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 27, 7, 3, 1, 1, 1, 1, 49, 109, 109, 49, 49, 123, 123, 123, 197, 201, 201, 201, 109, 109, 49, 49, 49, 7, 7, 3, 3, 1, 1, 1, 1, 1, 109, 109, 197, 201, 201, 109, 109] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 3, 4, 9, 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]) total number of confs: 893 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086543 none CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', '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, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 9, 32, 65, 109, 109, 1, 1, 1, 1, 1, 2, 2, 2, 7, 15, 21, 21, 1, 1, 5, 5, 5, 32, 32, 65, 65, 109, 109, 109, 109, 109, 1, 1, 7, 15, 15, 1, 1] 201 rigid atoms, others: [1, 35, 36, 40, 9, 10, 11, 12, 13, 21, 22, 41] set([0, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 529 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086543 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086543 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086543/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086543 Building REAL300000086544 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086544' /scratch/stefan/7769667/working/building/REAL300000086544 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086544 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086544/0 /scratch/stefan/7769667/working/building/REAL300000086544 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/569 `/scratch/stefan/7769667/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1) `REAL300000086544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086544 none CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 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, 6, 6, 4, 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, 7, 7] 0 hydrogens 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, 27, 7, 3, 1, 1, 1, 1, 33, 83, 83, 33, 34, 111, 111, 111, 150, 201, 201, 201, 201, 83, 83, 33, 33, 33, 7, 7, 3, 3, 1, 1, 1, 1, 1, 83, 83, 150, 201, 201, 201, 201, 83, 83] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 31] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 1021 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086544 none CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 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, 6, 6, 4, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 9, 29, 55, 83, 83, 1, 1, 1, 1, 1, 2, 2, 2, 5, 13, 13, 17, 17, 1, 1, 5, 5, 5, 29, 29, 55, 55, 83, 83, 83, 83, 83, 1, 1, 5, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [1, 43, 36, 37, 9, 10, 11, 12, 13, 44, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42]) total number of confs: 401 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086544 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086544 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086544/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086544 Building REAL300000086545 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086545' /scratch/stefan/7769667/working/building/REAL300000086545 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086545 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086545/0 /scratch/stefan/7769667/working/building/REAL300000086545 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/570 `/scratch/stefan/7769667/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)NCCCC(=O)[O-])C=C1) `REAL300000086545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086545 none CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)NCCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 1, 1, 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, 6, 6, 4, 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, 7, 7, 7, 7] 0 hydrogens 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, 27, 7, 3, 1, 1, 1, 1, 35, 83, 83, 35, 35, 107, 107, 107, 140, 200, 200, 201, 201, 201, 83, 83, 35, 35, 35, 7, 7, 3, 3, 1, 1, 1, 1, 1, 83, 83, 140, 200, 200, 200, 200, 201, 201, 83, 83] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 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, 47]) total number of confs: 992 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086545 none CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)NCCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 1, 1, 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, 6, 6, 4, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 9, 29, 55, 83, 83, 1, 1, 1, 1, 1, 2, 2, 2, 5, 19, 25, 26, 34, 34, 1, 1, 5, 5, 5, 29, 29, 55, 55, 83, 83, 83, 83, 83, 1, 1, 5, 19, 19, 25, 25, 26, 26, 1, 1] 201 rigid atoms, others: [1, 37, 38, 9, 10, 11, 12, 13, 46, 47, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 483 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086545 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086545 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086545/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086545 Building REAL300000086546 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086546' /scratch/stefan/7769667/working/building/REAL300000086546 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086546 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086546/0 /scratch/stefan/7769667/working/building/REAL300000086546 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/571 `/scratch/stefan/7769667/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1) `REAL300000086546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086546 none CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 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, 6, 6, 4, 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, 7] 0 hydrogens 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, 31, 7, 3, 1, 1, 1, 1, 65, 132, 132, 66, 74, 156, 156, 156, 167, 201, 201, 201, 201, 201, 132, 132, 65, 65, 65, 7, 7, 3, 3, 1, 1, 1, 1, 1, 132, 132, 167, 201, 201, 201, 132, 132] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 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]) total number of confs: 928 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086546 none CC(=NOCCC1CC1)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 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, 6, 6, 4, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 13, 54, 92, 132, 132, 1, 1, 1, 1, 1, 2, 2, 2, 4, 9, 9, 9, 13, 13, 1, 1, 6, 6, 6, 54, 54, 92, 92, 132, 132, 132, 132, 132, 1, 1, 4, 9, 9, 9, 1, 1] 201 rigid atoms, others: [1, 43, 37, 38, 9, 10, 11, 12, 13, 44, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 587 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086546 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086546 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086546/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086546 Building REAL300000086547 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086547' /scratch/stefan/7769667/working/building/REAL300000086547 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086547 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086547/0 /scratch/stefan/7769667/working/building/REAL300000086547 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/572 `/scratch/stefan/7769667/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(Br)C=C1C=NOCCC1CC1) `REAL300000086547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086547 none O=C([O-])COC1=CC=C(Br)C=C1C=NOCCC1CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 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: [33, 22, 33, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 29, 55, 82, 82, 22, 22, 1, 1, 1, 4, 29, 29, 55, 55, 82, 82, 82, 82, 82] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086547 none O=C([O-])COC1=CC=C(Br)C=C1C=NOCCC1CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 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: [201, 201, 201, 162, 82, 82, 82, 79, 82, 82, 82, 79, 79, 35, 7, 3, 1, 1, 1, 1, 201, 201, 82, 82, 82, 79, 7, 7, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 485 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086547 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086547 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086547/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086547 Building REAL300000086548 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086548' /scratch/stefan/7769667/working/building/REAL300000086548 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086548 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086548/0 /scratch/stefan/7769667/working/building/REAL300000086548 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/573 `/scratch/stefan/7769667/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NOCCC2CC2)=C1) `REAL300000086548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086548 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NOCCC2CC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'N.2', 'O.3', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 8, 17, 17, 31, 87, 154, 201, 201, 8, 1, 1, 1, 1, 3, 3, 8, 8, 8, 17, 88, 88, 153, 153, 201, 201, 201, 201, 201, 8] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 862 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: REAL300000086548 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NOCCC2CC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'N.2', 'O.3', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 127, 126, 89, 89, 89, 89, 89, 51, 51, 30, 7, 3, 1, 1, 1, 1, 89, 201, 201, 201, 201, 127, 127, 89, 89, 89, 51, 7, 7, 3, 3, 1, 1, 1, 1, 1, 89] 201 rigid atoms, others: [39, 40, 41, 42, 43, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44]) total number of confs: 362 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086548 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NOCCC2CC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'N.2', 'O.3', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 11, 8, 8, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 36, 59, 89, 89, 1, 8, 8, 8, 8, 4, 4, 1, 1, 1, 5, 37, 37, 58, 58, 89, 89, 89, 89, 89, 1] 201 rigid atoms, others: [32, 33, 44, 10, 11, 12, 13, 14, 15, 16, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 392 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086548 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086548 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086548/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086548 Building REAL300000086549 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086549' /scratch/stefan/7769667/working/building/REAL300000086549 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086549 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086549/0 /scratch/stefan/7769667/working/building/REAL300000086549 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/574 `/scratch/stefan/7769667/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NOCCC2CC2)C=C1[N+](=O)[O-]) `REAL300000086549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086549 none O=C([O-])COC1=CC=C(C=NOCCC2CC2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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 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, 5, 1, 1, 1, 1, 1, 1, 4, 4, 8, 32, 60, 90, 90, 1, 1, 1, 2, 2, 13, 13, 1, 1, 4, 32, 32, 60, 60, 90, 90, 90, 90, 90, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 18, 19, 24, 25, 36] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 412 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086549 none O=C([O-])COC1=CC=C(C=NOCCC2CC2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 136, 90, 86, 90, 90, 52, 52, 33, 7, 3, 1, 1, 1, 1, 90, 90, 90, 90, 90, 201, 201, 90, 90, 52, 7, 7, 3, 3, 1, 1, 1, 1, 1, 90] 201 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 658 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086549 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086549 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086549/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086549 Building REAL300000086550 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086550' /scratch/stefan/7769667/working/building/REAL300000086550 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086550 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086550/0 /scratch/stefan/7769667/working/building/REAL300000086550 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/575 `/scratch/stefan/7769667/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NOCCC3CC3)C=C2)=C1) `REAL300000086550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086550 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NOCCC3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.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, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 11, 11, 25, 77, 155, 201, 201, 6, 6, 1, 2, 2, 2, 6, 6, 6, 6, 11, 77, 77, 155, 155, 201, 201, 201, 201, 201, 5, 6, 1] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 44, 24] set([4, 5, 9, 10, 11, 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: 851 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086550 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NOCCC3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.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, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 73, 73, 73, 73, 73, 73, 40, 40, 29, 7, 3, 1, 1, 1, 1, 73, 73, 201, 201, 201, 201, 73, 73, 73, 73, 40, 7, 7, 3, 3, 1, 1, 1, 1, 1, 73, 73, 201] 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, 44]) total number of confs: 326 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086550 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NOCCC3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.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, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 11, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 23, 46, 73, 73, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 2, 23, 23, 46, 46, 73, 73, 73, 73, 73, 1, 1, 6] 201 rigid atoms, others: [43, 7, 8, 9, 10, 11, 12, 13, 14, 42, 22, 23, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086550 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086550 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086550/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086550 Building REAL300000086551 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086551' /scratch/stefan/7769667/working/building/REAL300000086551 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086551 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086551/0 /scratch/stefan/7769667/working/building/REAL300000086551 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/576 `/scratch/stefan/7769667/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(COC2=CC=CC(C=NOCCC3CC3)=C2)=C1) `REAL300000086551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086551 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NOCCC3CC3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', '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.2', 'N.2', 'O.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 6, 6, 11, 11, 11, 11, 11, 23, 23, 33, 80, 152, 201, 201, 11, 1, 1, 1, 1, 6, 6, 11, 11, 11, 23, 80, 80, 152, 152, 201, 201, 201, 201, 201, 11, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 44, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 853 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086551 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NOCCC3CC3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', '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.2', 'N.2', 'O.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 84, 84, 46, 46, 46, 46, 46, 32, 32, 24, 7, 3, 1, 1, 1, 1, 46, 201, 201, 201, 201, 84, 84, 46, 46, 46, 32, 7, 7, 3, 3, 1, 1, 1, 1, 1, 46, 201] 201 rigid atoms, others: [38, 39, 40, 41, 42, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44]) total number of confs: 347 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086551 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NOCCC3CC3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', '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.2', 'N.2', 'O.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 10, 11, 11, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 19, 34, 46, 46, 1, 11, 10, 11, 11, 2, 2, 1, 1, 1, 5, 19, 19, 34, 34, 46, 46, 46, 46, 46, 1, 11] 201 rigid atoms, others: [32, 43, 9, 10, 11, 12, 13, 14, 15, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44]) total number of confs: 207 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086551 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086551 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086551/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086551 Building REAL300000086552 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086552' /scratch/stefan/7769667/working/building/REAL300000086552 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086552 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086552/0 /scratch/stefan/7769667/working/building/REAL300000086552 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/577 `/scratch/stefan/7769667/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(COC2=CC=C(C=NOCCC3CC3)C=C2)OC=C1) `REAL300000086552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086552 none O=C([O-])C1=C(COC2=CC=C(C=NOCCC3CC3)C=C2)OC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 22, 22, 44, 99, 163, 201, 201, 9, 9, 1, 1, 1, 5, 5, 9, 10, 22, 99, 99, 163, 163, 201, 201, 201, 201, 201, 9, 9, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 40, 41, 21, 22, 23] set([0, 2, 6, 7, 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, 37, 38, 39]) total number of confs: 849 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: REAL300000086552 none O=C([O-])C1=C(COC2=CC=C(C=NOCCC3CC3)C=C2)OC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 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, 100, 83, 82, 80, 83, 83, 54, 54, 30, 7, 3, 1, 1, 1, 1, 83, 83, 201, 201, 201, 100, 100, 83, 83, 54, 7, 7, 3, 3, 1, 1, 1, 1, 1, 83, 83, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 15, 16, 17, 18] 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, 30, 31, 32, 38, 39, 40, 41]) total number of confs: 409 number of broken/clashed sets: 30 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086552 none O=C([O-])C1=C(COC2=CC=C(C=NOCCC3CC3)C=C2)OC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 11, 9, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 33, 61, 83, 83, 1, 1, 9, 9, 9, 5, 5, 1, 1, 4, 33, 33, 61, 61, 83, 83, 83, 83, 83, 1, 1, 9, 9] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38, 19, 20, 39, 26, 27] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 374 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086552 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086552 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086552/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086552 Building REAL300000086553 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086553' /scratch/stefan/7769667/working/building/REAL300000086553 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086553 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086553/0 /scratch/stefan/7769667/working/building/REAL300000086553 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/578 `/scratch/stefan/7769667/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NOCCC1CC1) `REAL300000086553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086553 none CN1C(C(=O)[O-])=CC(Br)=C1C=NOCCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 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, 2, 2, 1, 1, 1, 1, 1, 13, 13, 63, 138, 165, 201, 201, 2, 2, 2, 1, 13, 138, 138, 165, 165, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 21] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086553 none CN1C(C(=O)[O-])=CC(Br)=C1C=NOCCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 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: [201, 201, 201, 201, 201, 201, 201, 201, 201, 143, 143, 43, 7, 3, 1, 1, 1, 1, 201, 201, 201, 201, 143, 7, 7, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [14, 15, 16, 17, 27, 28, 29, 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]) total number of confs: 308 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086553 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086553 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086553/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086553 Building REAL300000086554 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086554' /scratch/stefan/7769667/working/building/REAL300000086554 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086554 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086554/0 /scratch/stefan/7769667/working/building/REAL300000086554 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/579 `/scratch/stefan/7769667/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NOCCC2CC2)C=C1Br) `REAL300000086554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086554 none O=C([O-])COC1=CC=C(C=NOCCC2CC2)C=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7] 0 hydrogens 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, 21, 31, 7, 1, 1, 1, 1, 1, 1, 2, 2, 6, 30, 55, 85, 85, 1, 1, 1, 21, 21, 1, 1, 2, 30, 30, 55, 55, 85, 85, 85, 85, 85, 1] 201 rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 449 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086554 none O=C([O-])COC1=CC=C(C=NOCCC2CC2)C=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 154, 85, 85, 85, 85, 54, 54, 32, 7, 3, 1, 1, 1, 1, 85, 85, 85, 201, 201, 85, 85, 54, 7, 7, 3, 3, 1, 1, 1, 1, 1, 85] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 531 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086554 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086554 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086554/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086554 Building REAL300000086555 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086555' /scratch/stefan/7769667/working/building/REAL300000086555 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086555 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086555/0 /scratch/stefan/7769667/working/building/REAL300000086555 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/580 `/scratch/stefan/7769667/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NOCCC2CC2)C=C1) `REAL300000086555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086555 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NOCCC2CC2)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', 'N.2', 'O.3', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 8, 28, 102, 150, 201, 201, 1, 1, 3, 3, 3, 1, 8, 102, 102, 150, 150, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 20, 21, 25, 37, 36] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 796 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086555 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NOCCC2CC2)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', 'N.2', 'O.3', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 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: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 137, 42, 7, 3, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 137, 7, 7, 3, 3, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086555 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086555 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086555/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086555 Building REAL300000086556 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086556' /scratch/stefan/7769667/working/building/REAL300000086556 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086556 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086556/0 /scratch/stefan/7769667/working/building/REAL300000086556 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/581 `/scratch/stefan/7769667/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN(CCOC2=CC=C(C=NOCCC3CC3)C=C2Cl)N=N1) `REAL300000086556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086556 none O=C([O-])C1=CN(CCOC2=CC=C(C=NOCCC3CC3)C=C2Cl)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 11, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 6, 10, 19, 33, 33, 19, 25, 53, 53, 53, 111, 191, 201, 201, 33, 33, 33, 1, 1, 1, 6, 6, 10, 10, 33, 33, 53, 111, 111, 191, 191, 201, 201, 201, 201, 201, 33] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 941 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086556 none O=C([O-])C1=CN(CCOC2=CC=C(C=NOCCC3CC3)C=C2Cl)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 11, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 139, 139, 119, 41, 41, 41, 41, 25, 25, 25, 7, 3, 1, 1, 1, 1, 41, 41, 41, 201, 201, 201, 139, 139, 139, 139, 41, 41, 25, 7, 7, 3, 3, 1, 1, 1, 1, 1, 41] 201 rigid atoms, others: [38, 39, 40, 41, 42, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43]) total number of confs: 432 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086556 none O=C([O-])C1=CN(CCOC2=CC=C(C=NOCCC3CC3)C=C2Cl)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 11, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 9, 9, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 24, 41, 41, 1, 1, 1, 33, 33, 33, 9, 9, 9, 9, 1, 1, 2, 10, 10, 24, 24, 41, 41, 41, 41, 41, 1] 201 rigid atoms, others: [32, 43, 8, 9, 10, 11, 12, 13, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 219 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086556 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086556 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086556/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086556 Building REAL300000086557 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086557' /scratch/stefan/7769667/working/building/REAL300000086557 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086557 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086557/0 /scratch/stefan/7769667/working/building/REAL300000086557 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/582 `/scratch/stefan/7769667/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NOCCC2CC2)=C([N+](=O)[O-])C=C1OCC(=O)[O-]) `REAL300000086557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086557 none COC1=CC(C=NOCCC2CC2)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [3, 1, 1, 1, 1, 1, 3, 3, 7, 31, 57, 81, 81, 1, 1, 2, 2, 1, 1, 1, 9, 13, 19, 19, 3, 3, 3, 1, 3, 31, 31, 57, 57, 81, 81, 81, 81, 81, 1, 13, 13] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 13, 14, 17, 18, 19, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 15, 16, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086557 none COC1=CC(C=NOCCC2CC2)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [114, 81, 81, 81, 57, 57, 29, 7, 3, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 81, 201, 201, 201, 201, 114, 114, 114, 81, 57, 7, 7, 3, 3, 1, 1, 1, 1, 1, 81, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 376 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086557 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086557 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086557/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086557 Building REAL300000086558 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086558' /scratch/stefan/7769667/working/building/REAL300000086558 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086558 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086558/0 /scratch/stefan/7769667/working/building/REAL300000086558 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/583 `/scratch/stefan/7769667/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NOCCC1CC1) `REAL300000086558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086558 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NOCCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 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: [4, 1, 4, 11, 16, 16, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 4, 4, 19, 78, 129, 164, 164, 4, 4, 4, 11, 11, 1, 1, 1, 4, 78, 78, 129, 129, 164, 164, 164, 164, 164] 201 rigid atoms, others: [1, 6, 7, 8, 9, 10, 14, 15, 16, 29, 30, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 727 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086558 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NOCCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 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: [182, 164, 182, 201, 201, 201, 164, 164, 137, 164, 164, 164, 164, 164, 164, 137, 137, 42, 7, 3, 1, 1, 1, 1, 182, 182, 182, 201, 201, 164, 164, 164, 137, 7, 7, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 557 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086558 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086558 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086558/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086558 Building REAL300000086559 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086559' /scratch/stefan/7769667/working/building/REAL300000086559 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086559 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086559/0 /scratch/stefan/7769667/working/building/REAL300000086559 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/584 `/scratch/stefan/7769667/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NOCCC1CC1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000086559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086559 none CC(=NOCCC1CC1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 30, 7, 3, 1, 1, 1, 1, 45, 79, 79, 61, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 79, 45, 45, 45, 7, 7, 3, 3, 1, 1, 1, 1, 1, 79, 79, 201, 201, 201, 201, 79, 79] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 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]) total number of confs: 397 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086559 none CC(=NOCCC1CC1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 10, 26, 26, 40, 99, 156, 201, 201, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 10, 10, 26, 26, 26, 99, 99, 156, 156, 201, 201, 201, 201, 201, 10, 10, 1, 1, 1, 1, 10, 10] 201 rigid atoms, others: [39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 821 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086559 none CC(=NOCCC1CC1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 11, 40, 58, 79, 79, 1, 1, 1, 1, 1, 9, 10, 10, 9, 10, 10, 10, 10, 10, 1, 1, 5, 5, 5, 40, 40, 58, 58, 79, 79, 79, 79, 79, 1, 1, 10, 10, 10, 10, 1, 1] 201 rigid atoms, others: [1, 43, 37, 38, 9, 10, 11, 12, 13, 44, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086559 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086559 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086559/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086559 Building REAL300000086560 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086560' /scratch/stefan/7769667/working/building/REAL300000086560 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086560 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086560/0 /scratch/stefan/7769667/working/building/REAL300000086560 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/585 `/scratch/stefan/7769667/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NOCCC2CC2)=CC=C1OCCC(=O)[O-]) `REAL300000086560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086560 none COC1=CC(C=NOCCC2CC2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens 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, 3, 7, 19, 37, 55, 55, 1, 1, 1, 1, 5, 9, 10, 15, 13, 3, 3, 3, 1, 3, 19, 19, 37, 37, 55, 55, 55, 55, 55, 1, 1, 9, 9, 9, 9] 201 rigid atoms, others: [1, 2, 3, 4, 5, 13, 14, 15, 16, 25, 37, 36] set([0, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086560 none COC1=CC(C=NOCCC2CC2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens 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, 55, 55, 55, 31, 31, 23, 7, 3, 1, 1, 1, 1, 55, 55, 55, 55, 136, 187, 187, 201, 174, 85, 85, 85, 55, 31, 7, 7, 3, 3, 1, 1, 1, 1, 1, 55, 55, 187, 187, 187, 187] 201 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41]) total number of confs: 596 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086560 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086560 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086560/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086560 Building REAL300000086561 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086561' /scratch/stefan/7769667/working/building/REAL300000086561 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086561 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086561/0 /scratch/stefan/7769667/working/building/REAL300000086561 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/586 `/scratch/stefan/7769667/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NOCCC1CC1)C1=CC=CC(OCCCC(=O)[O-])=C1) `REAL300000086561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086561 none CC(=NOCCC1CC1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 3, 1, 1, 1, 1, 15, 35, 35, 35, 35, 35, 92, 122, 138, 201, 201, 201, 35, 15, 15, 15, 7, 7, 3, 3, 1, 1, 1, 1, 1, 35, 35, 35, 122, 122, 138, 138, 201, 201, 35] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 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: 775 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086561 none CC(=NOCCC1CC1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 5, 12, 23, 35, 35, 1, 1, 1, 1, 1, 1, 7, 17, 21, 27, 32, 32, 1, 5, 5, 5, 12, 12, 23, 23, 35, 35, 35, 35, 35, 1, 1, 1, 17, 17, 21, 21, 27, 27, 1] 201 rigid atoms, others: [1, 34, 35, 36, 9, 10, 11, 12, 13, 14, 43, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 269 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086561 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086561 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086561/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086561 Building REAL300000086562 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086562' /scratch/stefan/7769667/working/building/REAL300000086562 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086562 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086562/0 /scratch/stefan/7769667/working/building/REAL300000086562 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/587 `/scratch/stefan/7769667/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)=NOCCC1CC1) `REAL300000086562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086562 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)=NOCCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', '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', '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'] dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [11, 4, 2, 1, 1, 1, 1, 1, 1, 7, 14, 14, 17, 17, 1, 1, 11, 11, 17, 39, 67, 102, 102, 11, 11, 11, 4, 4, 2, 2, 1, 1, 14, 14, 14, 14, 1, 1, 39, 39, 67, 67, 102, 102, 102, 102, 102] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 14, 15, 36, 37, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 491 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086562 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)=NOCCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', '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', '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'] dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [33, 33, 33, 96, 102, 102, 102, 102, 102, 175, 201, 201, 201, 201, 102, 102, 27, 7, 3, 1, 1, 1, 1, 33, 33, 33, 96, 96, 102, 102, 102, 102, 201, 201, 201, 201, 102, 102, 7, 7, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 631 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086562 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086562 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086562/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086562 Building REAL300000086563 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086563' /scratch/stefan/7769667/working/building/REAL300000086563 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086563 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086563/0 /scratch/stefan/7769667/working/building/REAL300000086563 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/588 `/scratch/stefan/7769667/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NOCCC1CC1) `REAL300000086563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086563 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NOCCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [12, 4, 2, 1, 1, 1, 1, 1, 1, 6, 14, 25, 25, 1, 1, 12, 12, 12, 32, 58, 92, 92, 12, 12, 12, 4, 4, 2, 2, 1, 1, 14, 14, 1, 1, 32, 32, 58, 58, 92, 92, 92, 92, 92] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 13, 14, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 468 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086563 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NOCCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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, 86, 92, 92, 92, 92, 92, 184, 201, 201, 201, 92, 92, 27, 7, 3, 1, 1, 1, 1, 27, 27, 27, 86, 86, 92, 92, 92, 92, 201, 201, 92, 92, 7, 7, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 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, 37, 38]) total number of confs: 577 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086563 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086563 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086563/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086563 Building REAL300000086564 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086564' /scratch/stefan/7769667/working/building/REAL300000086564 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086564 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086564/0 /scratch/stefan/7769667/working/building/REAL300000086564 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/589 `/scratch/stefan/7769667/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)=NOCCC1CC1) `REAL300000086564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086564 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)=NOCCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', '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', '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'] dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [11, 4, 2, 1, 1, 1, 1, 1, 1, 6, 8, 9, 15, 15, 1, 1, 11, 11, 14, 31, 50, 72, 72, 11, 11, 11, 4, 4, 2, 2, 1, 1, 8, 8, 8, 8, 1, 1, 31, 31, 50, 50, 72, 72, 72, 72, 72] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 14, 15, 36, 37, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086564 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)=NOCCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', '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', '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'] dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [27, 27, 27, 70, 72, 72, 72, 72, 72, 201, 201, 201, 201, 201, 72, 72, 25, 7, 3, 1, 1, 1, 1, 27, 27, 27, 70, 70, 72, 72, 72, 72, 201, 201, 201, 201, 72, 72, 7, 7, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 434 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086564 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086564 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086564/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086564 Building REAL300000086565 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086565' /scratch/stefan/7769667/working/building/REAL300000086565 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086565 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086565/0 /scratch/stefan/7769667/working/building/REAL300000086565 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/590 `/scratch/stefan/7769667/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)=NOCCC1CC1) `REAL300000086565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086565 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)=NOCCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 10, 10, 10, 10, 11, 11, 10, 1, 1, 12, 12, 12, 30, 53, 67, 67, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 10, 10, 10, 10, 1, 1, 30, 30, 53, 53, 67, 67, 67, 67, 67] 201 rigid atoms, others: [19, 33, 2, 3, 4, 5, 6, 7, 8, 43, 44, 34, 35, 20, 36] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086565 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)=NOCCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [27, 27, 27, 65, 67, 67, 67, 67, 67, 95, 95, 201, 201, 201, 201, 201, 201, 201, 201, 67, 67, 27, 7, 3, 1, 1, 1, 1, 27, 27, 27, 65, 65, 67, 67, 67, 67, 95, 95, 201, 201, 201, 201, 67, 67, 7, 7, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [49, 50, 51, 52, 53, 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, 22, 23, 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: 464 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086565 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)=NOCCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [55, 18, 10, 5, 5, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 10, 10, 55, 55, 55, 103, 177, 201, 201, 55, 55, 55, 18, 18, 10, 10, 10, 10, 5, 5, 1, 1, 1, 1, 10, 10, 103, 103, 177, 177, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 15, 18, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 907 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086565 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086565 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086565/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086565 Building REAL300000086566 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086566' /scratch/stefan/7769667/working/building/REAL300000086566 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086566 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086566/0 /scratch/stefan/7769667/working/building/REAL300000086566 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/591 `/scratch/stefan/7769667/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NOCCC1CC1)C1=CC=C(OCCCCC(=O)[O-])C=C1) `REAL300000086566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086566 none CCC(=NOCCC1CC1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 7, 3, 1, 1, 1, 1, 23, 58, 58, 31, 58, 153, 153, 157, 157, 157, 171, 171, 58, 58, 40, 40, 40, 40, 40, 7, 7, 3, 3, 1, 1, 1, 1, 1, 58, 58, 153, 153, 157, 157, 157, 157, 157, 157, 58, 58] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 499 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086566 none CCC(=NOCCC1CC1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 6, 6, 6, 19, 35, 58, 58, 1, 1, 1, 1, 1, 6, 6, 8, 8, 9, 15, 15, 1, 1, 9, 9, 9, 9, 9, 19, 19, 35, 35, 58, 58, 58, 58, 58, 1, 1, 6, 6, 8, 8, 9, 9, 8, 8, 1, 1] 201 rigid atoms, others: [2, 38, 39, 10, 11, 12, 13, 14, 48, 49, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 306 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086566 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086566 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086566/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086566 Building REAL300000086567 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086567' /scratch/stefan/7769667/working/building/REAL300000086567 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086567 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086567/0 /scratch/stefan/7769667/working/building/REAL300000086567 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/592 `/scratch/stefan/7769667/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NOCCC2CC2)=CC=C1OCCCC(=O)[O-]) `REAL300000086567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086567 none COC1=CC(C(C)=NOCCC2CC2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 9, 23, 42, 71, 71, 1, 1, 1, 1, 5, 9, 9, 15, 23, 23, 3, 3, 3, 1, 7, 7, 7, 23, 23, 42, 42, 71, 71, 71, 71, 71, 1, 1, 9, 9, 9, 9, 15, 15] 201 rigid atoms, others: [1, 2, 3, 4, 5, 40, 41, 14, 15, 16, 17, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 381 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086567 none COC1=CC(C(C)=NOCCC2CC2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 71, 71, 71, 29, 29, 29, 27, 7, 3, 1, 1, 1, 1, 71, 71, 71, 71, 132, 199, 199, 201, 201, 201, 112, 112, 112, 71, 29, 29, 29, 7, 7, 3, 3, 1, 1, 1, 1, 1, 71, 71, 199, 199, 199, 199, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 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, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 664 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086567 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086567 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086567/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086567 Building REAL300000086568 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086568' /scratch/stefan/7769667/working/building/REAL300000086568 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086568 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086568/0 /scratch/stefan/7769667/working/building/REAL300000086568 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/593 `/scratch/stefan/7769667/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NOCCC2CC2)C1) `REAL300000086568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086568 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NOCCC2CC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 8, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [3, 1, 3, 1, 1, 7, 7, 3, 7, 7, 7, 1, 1, 1, 1, 7, 41, 71, 107, 107, 1, 7, 7, 5, 7, 1, 1, 41, 41, 71, 71, 107, 107, 107, 107, 107, 1, 1] 201 rigid atoms, others: [1, 3, 4, 37, 11, 12, 13, 14, 20, 25, 26, 36] set([0, 2, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 469 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086568 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NOCCC2CC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 8, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [121, 107, 121, 107, 107, 201, 201, 191, 201, 201, 201, 107, 107, 32, 7, 3, 1, 1, 1, 1, 107, 201, 201, 201, 201, 107, 107, 7, 7, 3, 3, 1, 1, 1, 1, 1, 107, 107] 201 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37]) total number of confs: 441 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086568 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NOCCC2CC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 8, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 24, 92, 142, 201, 201, 7, 1, 1, 1, 1, 7, 7, 92, 92, 142, 142, 201, 201, 201, 201, 201, 7, 7] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 837 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086568 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086568 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086568/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086568 Building REAL300000086569 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086569' /scratch/stefan/7769667/working/building/REAL300000086569 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086569 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086569/0 /scratch/stefan/7769667/working/building/REAL300000086569 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/594 `/scratch/stefan/7769667/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=CC(Br)=C2)CC(=NOCCC2CC2)C1) `REAL300000086569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086569 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(=NOCCC2CC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 1, 8, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [3, 1, 3, 1, 1, 7, 7, 2, 7, 7, 7, 1, 1, 1, 1, 7, 41, 70, 104, 104, 1, 7, 7, 5, 7, 1, 1, 41, 41, 70, 70, 104, 104, 104, 104, 104, 1, 1] 201 rigid atoms, others: [1, 3, 4, 37, 11, 12, 13, 14, 20, 25, 26, 36] set([0, 2, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 460 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086569 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(=NOCCC2CC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 1, 8, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [118, 104, 118, 104, 104, 201, 201, 187, 201, 201, 201, 104, 104, 32, 7, 3, 1, 1, 1, 1, 104, 201, 201, 197, 201, 104, 104, 7, 7, 3, 3, 1, 1, 1, 1, 1, 104, 104] 201 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37]) total number of confs: 452 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086569 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(=NOCCC2CC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 1, 8, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [10, 7, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 23, 92, 142, 201, 201, 7, 1, 1, 1, 1, 7, 7, 92, 92, 142, 142, 201, 201, 201, 201, 201, 7, 7] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 836 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086569 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086569 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086569/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086569 Building REAL300000086570 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086570' /scratch/stefan/7769667/working/building/REAL300000086570 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086570 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086570/0 /scratch/stefan/7769667/working/building/REAL300000086570 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/595 `/scratch/stefan/7769667/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NOCCC1CC1)C1=CC(Br)=CC=C1OCC(=O)[O-]) `REAL300000086570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086570 none CC(=NOCCC1CC1)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [60, 60, 29, 7, 3, 1, 1, 1, 1, 60, 92, 92, 92, 60, 92, 92, 92, 179, 201, 201, 201, 60, 60, 60, 7, 7, 3, 3, 1, 1, 1, 1, 1, 92, 92, 92, 201, 201] 201 rigid atoms, others: [32, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086570 none CC(=NOCCC1CC1)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [3, 1, 3, 3, 7, 35, 55, 92, 92, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 22, 22, 3, 3, 3, 35, 35, 55, 55, 92, 92, 92, 92, 92, 1, 1, 1, 16, 16] 201 rigid atoms, others: [1, 34, 35, 33, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 447 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086570 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086570 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086570/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086570 Building REAL300000086571 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086571' /scratch/stefan/7769667/working/building/REAL300000086571 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086571 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086571/0 /scratch/stefan/7769667/working/building/REAL300000086571 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/596 `/scratch/stefan/7769667/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NOCCC1CC1)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1) `REAL300000086571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086571 none CC(=NOCCC1CC1)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [104, 104, 37, 7, 3, 1, 1, 1, 1, 104, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 104, 104, 7, 7, 3, 3, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 3, 4, 9, 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: 305 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086571 none CC(=NOCCC1CC1)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [9, 1, 9, 9, 35, 122, 153, 201, 201, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 122, 122, 153, 153, 201, 201, 201, 201, 201, 2, 2, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [1, 37, 38, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 42] set([0, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 808 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086571 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086571 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086571/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086571 Building REAL300000086572 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086572' /scratch/stefan/7769667/working/building/REAL300000086572 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086572 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086572/0 /scratch/stefan/7769667/working/building/REAL300000086572 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/597 `/scratch/stefan/7769667/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(OC1=CC=CC(C=NOCCC2CC2)=C1)C1=CC=CC=C1) `REAL300000086572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086572 none O=C([O-])C(OC1=CC=CC(C=NOCCC2CC2)=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 26, 9, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 20, 35, 51, 51, 1, 23, 31, 31, 23, 31, 31, 23, 1, 1, 1, 5, 20, 20, 35, 35, 51, 51, 51, 51, 51, 1, 31, 31, 23, 31, 31] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 39, 18, 26, 27, 28] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 334 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: REAL300000086572 none O=C([O-])C(OC1=CC=CC(C=NOCCC2CC2)=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 4, 1, 3, 8, 31, 31, 31, 31, 31, 44, 44, 52, 100, 177, 201, 201, 31, 1, 1, 1, 1, 1, 1, 3, 31, 31, 31, 44, 100, 100, 177, 177, 201, 201, 201, 201, 201, 31, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 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]) total number of confs: 833 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086572 none O=C([O-])C(OC1=CC=CC(C=NOCCC2CC2)=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 201, 129, 51, 51, 51, 51, 51, 36, 36, 27, 7, 3, 1, 1, 1, 1, 51, 199, 201, 201, 199, 201, 201, 199, 51, 51, 51, 36, 7, 7, 3, 3, 1, 1, 1, 1, 1, 51, 201, 201, 199, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 14, 15, 16, 17] 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, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44]) total number of confs: 574 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086572 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086572 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086572/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086572 Building REAL300000086573 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086573' /scratch/stefan/7769667/working/building/REAL300000086573 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086573 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086573/0 /scratch/stefan/7769667/working/building/REAL300000086573 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/598 `/scratch/stefan/7769667/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NOCCC1CC1)C1=CC(C(=O)[O-])=CC=C1OC(C)C) `REAL300000086573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086573 none CC(=NOCCC1CC1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [67, 67, 33, 7, 3, 1, 1, 1, 1, 67, 169, 169, 169, 169, 169, 169, 169, 169, 169, 201, 201, 201, 67, 67, 67, 7, 7, 3, 3, 1, 1, 1, 1, 1, 169, 169, 169, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 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: 312 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086573 none CC(=NOCCC1CC1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [7, 1, 7, 7, 15, 63, 107, 169, 169, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 7, 7, 7, 63, 63, 107, 107, 169, 169, 169, 169, 169, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [1, 34, 35, 36, 9, 10, 11, 12, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 716 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086573 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086573 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086573/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086573 Building REAL300000086574 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086574' /scratch/stefan/7769667/working/building/REAL300000086574 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086574 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086574/0 /scratch/stefan/7769667/working/building/REAL300000086574 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/599 `/scratch/stefan/7769667/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NOCCC3CC3)C=C2)C=C1) `REAL300000086574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086574 none O=C([O-])C1=CC=C(C2=CC=C(C=NOCCC3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 10, 10, 54, 111, 144, 164, 164, 3, 3, 1, 1, 1, 1, 3, 3, 10, 110, 111, 144, 144, 164, 164, 164, 164, 164, 3, 3, 1, 1] 164 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 21, 22, 23, 24, 39] set([0, 2, 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: 597 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: REAL300000086574 none O=C([O-])C1=CC=C(C2=CC=C(C=NOCCC3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 125, 164, 125, 164, 164, 124, 122, 125, 125, 119, 119, 44, 7, 3, 1, 1, 1, 1, 125, 125, 164, 164, 164, 164, 125, 125, 119, 7, 7, 3, 3, 1, 1, 1, 1, 1, 125, 125, 164, 164] 164 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18] 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, 30, 31, 37, 38, 39, 40]) total number of confs: 560 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086574 none O=C([O-])C1=CC=C(C2=CC=C(C=NOCCC3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 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: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 40, 93, 127, 148, 148, 1, 1, 3, 3, 3, 3, 1, 1, 9, 94, 94, 126, 126, 148, 148, 148, 148, 148, 1, 1, 3, 3] 164 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 563 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086574 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086574 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086574/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086574 Building REAL300000086575 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086575' /scratch/stefan/7769667/working/building/REAL300000086575 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086575 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086575/0 /scratch/stefan/7769667/working/building/REAL300000086575 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/600 `/scratch/stefan/7769667/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NOCCC2CC2)=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000086575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086575 none COC1=CC(C=NOCCC2CC2)=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', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens 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, 10, 40, 64, 88, 88, 1, 1, 1, 1, 1, 5, 8, 8, 10, 10, 4, 4, 4, 1, 5, 41, 41, 63, 63, 88, 88, 88, 88, 88, 1, 8, 8, 8, 8] 201 rigid atoms, others: [1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 26, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086575 none COC1=CC(C=NOCCC2CC2)=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', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 88, 88, 88, 53, 53, 30, 7, 3, 1, 1, 1, 1, 88, 88, 88, 88, 88, 168, 201, 201, 201, 201, 116, 116, 116, 88, 53, 7, 7, 3, 3, 1, 1, 1, 1, 1, 88, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41]) total number of confs: 515 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086575 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086575 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086575/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086575 Building REAL300000086576 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086576' /scratch/stefan/7769667/working/building/REAL300000086576 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086576 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086576/0 /scratch/stefan/7769667/working/building/REAL300000086576 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/601 `/scratch/stefan/7769667/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NOCCC3CC3)O2)=CC=C1O) `REAL300000086576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086576 none O=C([O-])C1=CC(C2=CC=C(C=NOCCC3CC3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 22, 20, 46, 101, 149, 201, 201, 13, 1, 1, 1, 1, 1, 13, 13, 22, 101, 101, 149, 149, 201, 201, 201, 201, 201, 1, 1, 2] 402 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 36, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 810 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086576 none O=C([O-])C1=CC(C2=CC=C(C=NOCCC3CC3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [201, 201, 201, 201, 201, 117, 117, 117, 117, 82, 82, 34, 7, 3, 1, 1, 1, 1, 117, 201, 201, 201, 201, 201, 117, 117, 82, 7, 7, 3, 3, 1, 1, 1, 1, 1, 201, 201, 402] 402 rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 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, 30, 36, 37, 38]) total number of confs: 717 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086576 none O=C([O-])C1=CC(C2=CC=C(C=NOCCC3CC3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [16, 13, 16, 13, 13, 1, 1, 1, 1, 1, 1, 4, 4, 12, 54, 84, 117, 117, 1, 13, 13, 12, 12, 13, 1, 1, 4, 54, 54, 84, 84, 117, 117, 117, 117, 117, 13, 13, 26] 402 rigid atoms, others: [5, 6, 7, 8, 9, 10, 18, 24, 25] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 523 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086576 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086576 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086576/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086576 Building REAL300000086577 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086577' /scratch/stefan/7769667/working/building/REAL300000086577 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086577 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086577/0 /scratch/stefan/7769667/working/building/REAL300000086577 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/602 `/scratch/stefan/7769667/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NOCCC3CC3)S2)C=C1) `REAL300000086577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086577 none O=C([O-])C1=CC=C(C2=CC=C(C=NOCCC3CC3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 32, 32, 63, 125, 165, 201, 201, 7, 1, 1, 1, 1, 7, 7, 32, 125, 125, 165, 165, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 36, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 777 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086577 none O=C([O-])C1=CC=C(C2=CC=C(C=NOCCC3CC3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [201, 139, 201, 139, 201, 201, 139, 139, 139, 139, 87, 87, 38, 7, 3, 1, 1, 1, 1, 139, 201, 201, 201, 201, 139, 139, 87, 7, 7, 3, 3, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 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, 30, 36, 37]) total number of confs: 742 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086577 none O=C([O-])C1=CC=C(C2=CC=C(C=NOCCC3CC3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 20, 67, 104, 139, 139, 1, 7, 7, 7, 7, 1, 1, 6, 67, 67, 104, 104, 139, 139, 139, 139, 139, 7, 7] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 599 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086577 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086577 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086577/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086577 Building REAL300000086578 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086578' /scratch/stefan/7769667/working/building/REAL300000086578 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086578 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086578/0 /scratch/stefan/7769667/working/building/REAL300000086578 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/603 `/scratch/stefan/7769667/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=NOCCC3CC3)S2)=C1) `REAL300000086578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086578 none O=C([O-])C1=CC=CC(C2=CC=C(C=NOCCC3CC3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 1, 1, 1, 1, 1, 12, 12, 12, 12, 32, 32, 51, 97, 150, 201, 201, 12, 1, 1, 1, 1, 12, 12, 32, 97, 97, 150, 150, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 811 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086578 none O=C([O-])C1=CC=CC(C2=CC=C(C=NOCCC3CC3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [201, 201, 201, 201, 201, 201, 201, 127, 127, 127, 127, 81, 81, 35, 7, 3, 1, 1, 1, 1, 127, 201, 201, 201, 201, 127, 127, 81, 7, 7, 3, 3, 1, 1, 1, 1, 1, 201] 201 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]) total number of confs: 336 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086578 none O=C([O-])C1=CC=CC(C2=CC=C(C=NOCCC3CC3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 5, 5, 13, 49, 93, 127, 127, 1, 12, 12, 12, 12, 1, 1, 5, 49, 49, 93, 93, 127, 127, 127, 127, 127, 12] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 543 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086578 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086578 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086578/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086578 Building REAL300000086579 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086579' /scratch/stefan/7769667/working/building/REAL300000086579 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086579 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086579/0 /scratch/stefan/7769667/working/building/REAL300000086579 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/604 `/scratch/stefan/7769667/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Br)C(C=NOCCC2CC2)=C1) `REAL300000086579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086579 none O=C([O-])C1=CC=C(Br)C(C=NOCCC2CC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 12, 12, 56, 126, 156, 201, 201, 1, 1, 1, 12, 126, 126, 156, 156, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 747 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086579 none O=C([O-])C1=CC=C(Br)C(C=NOCCC2CC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [201, 201, 201, 201, 201, 201, 201, 201, 137, 137, 41, 7, 3, 1, 1, 1, 1, 201, 201, 201, 137, 7, 7, 3, 3, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [13, 14, 15, 16, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 30]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086579 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086579 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086579/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086579 Building REAL300000086580 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086580' /scratch/stefan/7769667/working/building/REAL300000086580 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086580 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086580/0 /scratch/stefan/7769667/working/building/REAL300000086580 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/605 `/scratch/stefan/7769667/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(Br)=C(O)C(C=NOCCC2CC2)=C1) `REAL300000086580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086580 none O=C([O-])C1=CC(Br)=C(O)C(C=NOCCC2CC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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] 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, 1, 1, 1, 1, 1, 1, 1, 13, 13, 53, 119, 152, 201, 201, 1, 1, 2, 13, 119, 119, 152, 152, 201, 201, 201, 201, 201, 1] 402 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 31] set([11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 760 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086580 none O=C([O-])C1=CC(Br)=C(O)C(C=NOCCC2CC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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] 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: [201, 201, 201, 201, 201, 201, 201, 201, 201, 136, 136, 43, 7, 3, 1, 1, 1, 1, 201, 201, 402, 136, 7, 7, 3, 3, 1, 1, 1, 1, 1, 201] 402 rigid atoms, others: [14, 15, 16, 17, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 703 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086580 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086580/1 /scratch/stefan/7769667/working/building/REAL300000086580 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/606 `/scratch/stefan/7769667/working/3D/606' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(Br)=C([O-])C(C=NOCCC2CC2)=C1) `REAL300000086580.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086580 none O=C([O-])C1=CC(Br)=C([O-])C(C=NOCCC2CC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 34, 72, 99, 126, 126, 1, 1, 6, 72, 72, 99, 99, 126, 126, 126, 126, 126, 1] 126 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 30] set([11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 478 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086580 none O=C([O-])C1=CC(Br)=C([O-])C(C=NOCCC2CC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 126, 126, 126, 126, 126, 126, 118, 118, 39, 7, 3, 1, 1, 1, 1, 126, 126, 118, 7, 7, 3, 3, 1, 1, 1, 1, 1, 126] 126 rigid atoms, others: [14, 15, 16, 17, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 30]) total number of confs: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086580 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086580 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086580/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086580/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086580 Building REAL300000086581 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086581' /scratch/stefan/7769667/working/building/REAL300000086581 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086581 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086581/0 /scratch/stefan/7769667/working/building/REAL300000086581 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/607 `/scratch/stefan/7769667/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=CC(C=NOCCC2CC2)=C1OCC(=O)[O-]) `REAL300000086581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086581 none COC1=CC(Br)=CC(C=NOCCC2CC2)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 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, 3, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 44, 78, 105, 105, 1, 1, 2, 10, 23, 23, 3, 3, 3, 1, 1, 4, 44, 44, 78, 78, 105, 105, 105, 105, 105, 10, 10] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 503 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086581 none COC1=CC(Br)=CC(C=NOCCC2CC2)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 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, 3, 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: [154, 105, 105, 105, 105, 105, 105, 93, 93, 33, 7, 3, 1, 1, 1, 1, 105, 105, 154, 201, 201, 201, 154, 154, 154, 105, 105, 93, 7, 7, 3, 3, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 626 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086581 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086581 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086581/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086581 Building REAL300000086582 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086582' /scratch/stefan/7769667/working/building/REAL300000086582 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086582 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086582/0 /scratch/stefan/7769667/working/building/REAL300000086582 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/608 `/scratch/stefan/7769667/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(COC2=CC=C(C=NOCCC3CC3)C=C2)O1) `REAL300000086582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086582 none O=C([O-])C1=CC=C(COC2=CC=C(C=NOCCC3CC3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 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, 7] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 7, 7, 8, 8, 8, 8, 29, 29, 45, 119, 162, 201, 201, 8, 8, 1, 1, 1, 7, 7, 8, 8, 29, 119, 119, 162, 162, 201, 201, 201, 201, 201, 8, 8] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 23, 24, 25] set([0, 2, 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, 38, 39, 40, 41]) total number of confs: 814 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086582 none O=C([O-])C1=CC=C(COC2=CC=C(C=NOCCC3CC3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 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, 7] 0 hydrogens need rotated 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, 131, 131, 131, 121, 131, 131, 74, 74, 36, 7, 3, 1, 1, 1, 1, 131, 131, 201, 201, 201, 131, 131, 131, 131, 74, 7, 7, 3, 3, 1, 1, 1, 1, 1, 131, 131] 201 rigid atoms, others: [35, 36, 37, 38, 39, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 399 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086582 none O=C([O-])C1=CC=C(COC2=CC=C(C=NOCCC3CC3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 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, 7] 0 hydrogens 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, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 17, 56, 96, 131, 131, 1, 1, 8, 8, 8, 2, 2, 1, 1, 6, 56, 56, 95, 95, 131, 131, 131, 131, 131, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 40, 21, 22, 41, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 548 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086582 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086582 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086582/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086582 Building REAL300000086583 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086583' /scratch/stefan/7769667/working/building/REAL300000086583 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086583 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086583/0 /scratch/stefan/7769667/working/building/REAL300000086583 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/609 `/scratch/stefan/7769667/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(I)=CC(C=NOCCC2CC2)=C1) `REAL300000086583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086583 none O=C([O-])C1=CC(I)=CC(C=NOCCC2CC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 18, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 1, 1, 1, 1, 1, 1, 12, 12, 52, 115, 158, 201, 201, 1, 1, 1, 12, 115, 115, 158, 158, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 30] set([10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 767 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086583 none O=C([O-])C1=CC(I)=CC(C=NOCCC2CC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 18, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [201, 201, 201, 201, 201, 201, 201, 201, 130, 130, 43, 7, 3, 1, 1, 1, 1, 201, 201, 201, 130, 7, 7, 3, 3, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [13, 14, 15, 16, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 30]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086583 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086583 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086583/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086583 Building REAL300000086584 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086584' /scratch/stefan/7769667/working/building/REAL300000086584 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086584 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086584/0 /scratch/stefan/7769667/working/building/REAL300000086584 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/610 `/scratch/stefan/7769667/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(C=NOCCC3CC3)C=C2)=C1) `REAL300000086584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086584 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NOCCC3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 13, 13, 31, 83, 120, 151, 151, 3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 13, 83, 83, 120, 120, 151, 151, 151, 151, 151, 3, 3, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 43, 23, 26, 27, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 641 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086584 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NOCCC3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7] 0 hydrogens need rotated 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, 151, 151, 98, 151, 151, 98, 92, 98, 98, 58, 58, 33, 7, 3, 1, 1, 1, 1, 98, 98, 151, 201, 201, 98, 151, 151, 98, 98, 58, 7, 7, 3, 3, 1, 1, 1, 1, 1, 98, 98, 151] 201 rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43]) total number of confs: 770 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086584 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NOCCC3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 16, 51, 77, 98, 98, 1, 1, 3, 5, 5, 1, 3, 3, 1, 1, 6, 51, 51, 77, 77, 98, 98, 98, 98, 98, 1, 1, 3] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 42, 21, 22, 41, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 440 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086584 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086584 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086584/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086584 Building REAL300000086585 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086585' /scratch/stefan/7769667/working/building/REAL300000086585 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086585 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086585/0 /scratch/stefan/7769667/working/building/REAL300000086585 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/611 `/scratch/stefan/7769667/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NOCCC2CC2)=CC=C1OCC(=O)[O-]) `REAL300000086585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086585 none CCOC1=CC(C=NOCCC2CC2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 3, 3, 7, 17, 31, 47, 47, 1, 1, 1, 1, 7, 15, 25, 25, 5, 5, 5, 5, 5, 1, 3, 17, 17, 31, 31, 47, 47, 47, 47, 47, 1, 1, 15, 15] 201 rigid atoms, others: [2, 3, 4, 5, 6, 39, 38, 14, 15, 16, 17, 27] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086585 none CCOC1=CC(C=NOCCC2CC2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 81, 47, 47, 47, 31, 31, 23, 7, 3, 1, 1, 1, 1, 47, 47, 47, 47, 163, 199, 199, 199, 83, 83, 83, 83, 83, 47, 31, 7, 7, 3, 3, 1, 1, 1, 1, 1, 47, 47, 199, 199] 201 rigid atoms, others: [33, 34, 35, 36, 37, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41]) total number of confs: 542 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086585 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086585 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086585/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086585 Building REAL300000086586 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086586' /scratch/stefan/7769667/working/building/REAL300000086586 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086586 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086586/0 /scratch/stefan/7769667/working/building/REAL300000086586 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/612 `/scratch/stefan/7769667/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NN(C2CCOCC2)C=C1C=NOCCC1CC1) `REAL300000086586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086586 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NOCCC1CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 4, 4, 13, 45, 72, 102, 102, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 4, 45, 45, 72, 72, 102, 102, 102, 102, 102] 201 rigid atoms, others: [1, 3, 4, 5, 6, 12, 13, 14, 31] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 443 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086586 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NOCCC1CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 100, 102, 102, 102, 201, 201, 201, 201, 201, 102, 99, 99, 35, 7, 3, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 102, 99, 7, 7, 3, 3, 1, 1, 1, 1, 1] 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]) total number of confs: 475 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086586 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NOCCC1CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 18, 18, 59, 122, 158, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 18, 122, 122, 158, 158, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 746 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086586 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086586 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086586/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086586 Building REAL300000086587 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086587' /scratch/stefan/7769667/working/building/REAL300000086587 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086587 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086587/0 /scratch/stefan/7769667/working/building/REAL300000086587 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/613 `/scratch/stefan/7769667/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C2=CC=C(F)C=C2C(C=NOCCC2CC2)=C1C(=O)[O-]) `REAL300000086587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086587 none CN1C2=CC=C(F)C=C2C(C=NOCCC2CC2)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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, 1, 1, 1, 1, 1, 1, 1, 6, 6, 35, 103, 140, 176, 176, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 6, 103, 103, 140, 140, 176, 176, 176, 176, 176] 176 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 686 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086587 none CN1C2=CC=C(F)C=C2C(C=NOCCC2CC2)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 176, 176, 176, 176, 176, 176, 176, 144, 144, 44, 7, 3, 1, 1, 1, 1, 176, 176, 176, 176, 176, 176, 176, 176, 176, 176, 144, 7, 7, 3, 3, 1, 1, 1, 1, 1] 176 rigid atoms, others: [33, 34, 35, 36, 37, 14, 15, 16, 17] 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, 30, 31, 32]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086587 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086587 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086587/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086587 Building REAL300000086588 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086588' /scratch/stefan/7769667/working/building/REAL300000086588 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086588 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086588/0 /scratch/stefan/7769667/working/building/REAL300000086588 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/614 `/scratch/stefan/7769667/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NOCCC1CC1)C1=C(C(=O)[O-])C2=CC=CC=C2S1) `REAL300000086588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086588 none CC(=NOCCC1CC1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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, 7, 7] 0 hydrogens 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, 41, 7, 3, 1, 1, 1, 1, 130, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 130, 130, 130, 7, 7, 3, 3, 1, 1, 1, 1, 1, 201, 201, 201, 201] 201 rigid atoms, others: [32, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086588 none CC(=NOCCC1CC1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 27, 103, 153, 201, 201, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 103, 103, 153, 153, 201, 201, 201, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 33, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 806 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086588 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086588 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086588/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086588 Building REAL300000086589 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086589' /scratch/stefan/7769667/working/building/REAL300000086589 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086589 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086589/0 /scratch/stefan/7769667/working/building/REAL300000086589 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/615 `/scratch/stefan/7769667/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(C=NOCCC2CC2)SC(Br)=C1) `REAL300000086589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086589 none O=C([O-])C1=C(C=NOCCC2CC2)SC(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 14, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [3, 1, 3, 1, 1, 1, 5, 5, 33, 97, 135, 172, 172, 1, 1, 1, 1, 5, 97, 97, 135, 135, 172, 172, 172, 172, 172, 1] 201 rigid atoms, others: [1, 3, 4, 5, 13, 14, 15, 16, 27] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 664 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086589 none O=C([O-])C1=C(C=NOCCC2CC2)SC(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 14, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [201, 172, 201, 172, 161, 161, 45, 7, 3, 1, 1, 1, 1, 172, 172, 172, 172, 161, 7, 7, 3, 3, 1, 1, 1, 1, 1, 172] 201 rigid atoms, others: [9, 10, 11, 12, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27]) total number of confs: 364 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086589 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086589 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086589/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086589 Building REAL300000086590 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086590' /scratch/stefan/7769667/working/building/REAL300000086590 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086590 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086590/0 /scratch/stefan/7769667/working/building/REAL300000086590 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/616 `/scratch/stefan/7769667/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NOCCC2CC2)O1) `REAL300000086590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086590 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NOCCC2CC2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 5, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 85, 151, 201, 201, 1, 1, 1, 5, 5, 37, 37, 37, 37, 37, 85, 85, 151, 151, 201, 201, 201, 201, 201] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 23, 24, 25] set([0, 2, 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, 38, 39, 40, 41]) total number of confs: 824 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086590 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NOCCC2CC2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 135, 54, 23, 23, 23, 23, 23, 23, 23, 23, 23, 7, 3, 1, 1, 1, 1, 201, 201, 201, 135, 135, 23, 23, 23, 23, 23, 7, 7, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 555 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086590 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NOCCC2CC2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 37, 37, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 14, 23, 23, 37, 37, 37, 15, 15, 1, 1, 1, 1, 2, 6, 6, 14, 14, 23, 23, 23, 23, 23] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 174 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086590 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086590 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086590/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086590 Building REAL300000086591 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086591' /scratch/stefan/7769667/working/building/REAL300000086591 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086591 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086591/0 /scratch/stefan/7769667/working/building/REAL300000086591 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/617 `/scratch/stefan/7769667/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Br)C=CC=C1C=NOCCC1CC1) `REAL300000086591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086591 none O=C([O-])C1=C(Br)C=CC=C1C=NOCCC1CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 34, 79, 108, 129, 129, 1, 1, 1, 6, 79, 79, 108, 108, 129, 129, 129, 129, 129] 129 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 494 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086591 none O=C([O-])C1=C(Br)C=CC=C1C=NOCCC1CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 129, 129, 129, 129, 129, 129, 126, 126, 45, 7, 3, 1, 1, 1, 1, 129, 129, 129, 126, 7, 7, 3, 3, 1, 1, 1, 1, 1] 129 rigid atoms, others: [14, 15, 16, 17, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086591 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086591 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086591/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086591 Building REAL300000086592 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086592' /scratch/stefan/7769667/working/building/REAL300000086592 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086592 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086592/0 /scratch/stefan/7769667/working/building/REAL300000086592 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/618 `/scratch/stefan/7769667/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NOCCC1CC1) `REAL300000086592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086592 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NOCCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 23, 94, 145, 189, 189, 3, 3, 3, 1, 4, 4, 4, 1, 1, 7, 94, 94, 145, 145, 189, 189, 189, 189, 189] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 15, 16, 27, 31] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 770 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086592 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NOCCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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: [201, 189, 189, 189, 189, 189, 201, 189, 189, 189, 189, 189, 189, 189, 189, 135, 135, 37, 7, 3, 1, 1, 1, 1, 201, 201, 201, 189, 201, 201, 201, 189, 189, 135, 7, 7, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086592 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086592 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086592/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086592 Building REAL300000086593 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086593' /scratch/stefan/7769667/working/building/REAL300000086593 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086593 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086593/0 /scratch/stefan/7769667/working/building/REAL300000086593 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/619 `/scratch/stefan/7769667/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNS(=O)(=O)C1=CC=C(C=NOCCC2CC2)C=C1) `REAL300000086593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086593 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NOCCC2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 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: [9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 16, 63, 100, 133, 133, 1, 1, 9, 9, 5, 1, 1, 6, 63, 63, 100, 100, 133, 133, 133, 133, 133, 1, 1] 201 rigid atoms, others: [5, 38, 8, 9, 10, 11, 12, 20, 21, 25, 26, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086593 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NOCCC2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 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: [201, 201, 201, 183, 133, 119, 133, 133, 117, 133, 133, 79, 79, 37, 7, 3, 1, 1, 1, 1, 133, 133, 201, 201, 183, 133, 133, 79, 7, 7, 3, 3, 1, 1, 1, 1, 1, 133, 133] 201 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 654 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086593 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086593 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086593/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086593 Building REAL300000086594 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086594' /scratch/stefan/7769667/working/building/REAL300000086594 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086594 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086594/0 /scratch/stefan/7769667/working/building/REAL300000086594 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/620 `/scratch/stefan/7769667/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=NOCCC3CC3)C(F)=CC=C2S1) `REAL300000086594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086594 none O=C([O-])C1=CC2=C(C=NOCCC3CC3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 12, 56, 117, 160, 201, 201, 1, 1, 1, 1, 1, 1, 1, 12, 117, 117, 160, 160, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 747 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086594 none O=C([O-])C1=CC2=C(C=NOCCC3CC3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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: [201, 201, 201, 201, 201, 200, 117, 117, 39, 7, 3, 1, 1, 1, 1, 201, 201, 201, 201, 201, 199, 201, 117, 7, 7, 3, 3, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33]) total number of confs: 302 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086594 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086594 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086594/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086594 Building REAL300000086595 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086595' /scratch/stefan/7769667/working/building/REAL300000086595 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086595 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086595/0 /scratch/stefan/7769667/working/building/REAL300000086595 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/621 `/scratch/stefan/7769667/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNCC1(C)CCCC1)CCC2) `REAL300000086595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086595 none CC1=C(C(=O)[O-])OC2=C1C(=NNCC1(C)CCCC1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 7, 37, 80, 80, 80, 80, 80, 1, 1, 1, 2, 2, 2, 7, 37, 37, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1] 80 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 44, 40, 19, 20, 21, 43, 41, 39, 42] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 266 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086595 none CC1=C(C(=O)[O-])OC2=C1C(=NNCC1(C)CCCC1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 26, 7, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 80, 26, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 80] 80 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 149 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086595 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086595 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086595/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086595 Building REAL300000086596 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086596' /scratch/stefan/7769667/working/building/REAL300000086596 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086596 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086596/0 /scratch/stefan/7769667/working/building/REAL300000086596 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/622 `/scratch/stefan/7769667/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC(Br)=CC=C2OCC(=O)[O-])CCCC1) `REAL300000086596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086596 none CC1(CNN=CC2=CC(Br)=CC=C2OCC(=O)[O-])CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 6, 16, 45, 45, 78, 78, 78, 45, 78, 78, 78, 153, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 6, 6, 16, 45, 78, 78, 78, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 34, 18, 19, 20, 21] set([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]) total number of confs: 679 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086596 none CC1(CNN=CC2=CC(Br)=CC=C2OCC(=O)[O-])CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 38, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 34, 60, 60, 78, 78, 78, 78, 78, 78, 78, 38, 38, 14, 4, 1, 1, 1, 34, 34, 78, 78, 78, 78, 78, 78, 78, 78] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 454 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086596 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086596 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086596/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086596 Building REAL300000086597 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086597' /scratch/stefan/7769667/working/building/REAL300000086597 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086597 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086597/0 /scratch/stefan/7769667/working/building/REAL300000086597 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/623 `/scratch/stefan/7769667/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=NNCC2(C)CCCC2)=C1)C(=O)[O-]) `REAL300000086597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086597 none CC(OC1=CC=CC(C=NNCC2(C)CCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 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, 3, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 28, 56, 56, 56, 56, 56, 1, 27, 37, 37, 27, 27, 27, 27, 1, 1, 1, 5, 9, 28, 28, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 44, 18, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 307 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086597 none CC(OC1=CC=CC(C=NNCC2(C)CCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 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, 3, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 136, 56, 56, 56, 56, 56, 35, 35, 15, 5, 1, 1, 1, 1, 1, 1, 1, 56, 201, 201, 201, 201, 201, 201, 201, 56, 56, 56, 35, 15, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 56] 201 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44]) total number of confs: 561 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086597 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086597 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086597/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086597 Building REAL300000086598 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086598' /scratch/stefan/7769667/working/building/REAL300000086598 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086598 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086598/0 /scratch/stefan/7769667/working/building/REAL300000086598 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/624 `/scratch/stefan/7769667/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC=CC(OCCC(=O)[O-])=C2)CCCC1) `REAL300000086598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086598 none CC1(CNN=CC2=CC=CC(OCCC(=O)[O-])=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 5, 5, 5, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 4, 10, 24, 24, 60, 60, 60, 60, 60, 135, 181, 201, 201, 197, 60, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 24, 60, 60, 60, 181, 181, 201, 201, 60, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 41, 42, 43, 44, 18, 19, 20, 21] set([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]) total number of confs: 559 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086598 none CC1(CNN=CC2=CC=CC(OCCC(=O)[O-])=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 5, 5, 5, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 20, 28, 42, 36, 1, 60, 60, 60, 60, 60, 60, 60, 36, 36, 14, 6, 1, 1, 1, 20, 20, 28, 28, 1, 60, 60, 60, 60, 60, 60, 60, 60] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 365 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086598 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086598 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086598/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086598 Building REAL300000086599 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086599' /scratch/stefan/7769667/working/building/REAL300000086599 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086599 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086599/0 /scratch/stefan/7769667/working/building/REAL300000086599 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/625 `/scratch/stefan/7769667/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)CCCC1) `REAL300000086599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086599 none CC1(CNN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.2', 'O.co2', 'O.co2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 5, 12, 28, 28, 72, 72, 72, 72, 72, 100, 107, 201, 201, 201, 201, 201, 201, 201, 201, 72, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 28, 72, 72, 72, 107, 107, 201, 201, 201, 201, 72, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 44, 45, 46, 47, 48, 49, 50, 51, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 362 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: REAL300000086599 none CC1(CNN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.2', 'O.co2', 'O.co2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 159, 68, 36, 36, 15, 15, 15, 15, 15, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 201, 201, 201, 201, 201, 201, 201, 159, 159, 68, 36, 15, 14, 15, 6, 6, 1, 1, 1, 1, 15, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 40, 41, 42, 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, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 792 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086599 none CC1(CNN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.2', 'O.co2', 'O.co2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 42, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 6, 15, 15, 14, 15, 15, 15, 17, 17, 1, 72, 72, 72, 72, 72, 72, 72, 42, 42, 15, 6, 1, 1, 1, 6, 6, 15, 15, 14, 15, 1, 72, 72, 72, 72, 72, 72, 72, 72] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 43, 22] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 311 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086599 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086599 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086599/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086599 Building REAL300000086600 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086600' /scratch/stefan/7769667/working/building/REAL300000086600 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086600 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086600/0 /scratch/stefan/7769667/working/building/REAL300000086600 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/626 `/scratch/stefan/7769667/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)CCCC1) `REAL300000086600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086600 none CC1(CNN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 6, 15, 30, 30, 64, 64, 54, 64, 86, 86, 86, 86, 64, 64, 64, 64, 64, 1, 1, 1, 1, 2, 2, 2, 6, 6, 15, 30, 64, 64, 86, 86, 64, 1, 1, 1, 1, 1, 1, 1, 1] 86 rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 40, 41, 42, 43, 20, 21, 22, 23] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086600 none CC1(CNN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [64, 44, 18, 7, 7, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 1, 1, 2, 2, 1, 64, 64, 64, 64, 64, 64, 64, 44, 44, 18, 7, 1, 1, 5, 5, 1, 64, 64, 64, 64, 64, 64, 64, 64] 86 rigid atoms, others: [32, 35, 5, 6, 7, 8, 9, 10, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086600 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086600 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086600/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086600 Building REAL300000086601 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086601' /scratch/stefan/7769667/working/building/REAL300000086601 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086601 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086601/0 /scratch/stefan/7769667/working/building/REAL300000086601 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/627 `/scratch/stefan/7769667/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNCC3(C)CCCC3)C=C2)=C1) `REAL300000086601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086601 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNCC3(C)CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', '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, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 9, 9, 9, 28, 28, 62, 128, 201, 201, 201, 201, 201, 9, 9, 1, 2, 2, 2, 9, 9, 9, 9, 28, 62, 128, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 8, 9, 1] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 51, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 760 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086601 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNCC3(C)CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', '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, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 92, 92, 68, 66, 92, 92, 39, 39, 15, 5, 1, 1, 1, 1, 1, 1, 1, 92, 92, 201, 201, 201, 201, 92, 92, 92, 92, 39, 15, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 92, 92, 201] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 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, 37, 38, 39, 40, 49, 50, 51]) total number of confs: 448 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086601 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNCC3(C)CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', '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, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 14, 14, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 44, 92, 92, 92, 92, 92, 1, 1, 9, 9, 9, 9, 2, 1, 1, 1, 6, 19, 44, 44, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 1, 1, 9] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 49, 50, 24, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51]) total number of confs: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086601 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086601 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086601/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086601 Building REAL300000086602 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086602' /scratch/stefan/7769667/working/building/REAL300000086602 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086602 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086602/0 /scratch/stefan/7769667/working/building/REAL300000086602 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/628 `/scratch/stefan/7769667/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)CCCC1) `REAL300000086602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086602 none CC1(CNN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.2', 'O.co2', 'O.co2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 5, 12, 24, 24, 29, 29, 29, 29, 29, 52, 52, 201, 201, 201, 201, 201, 201, 201, 201, 29, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 24, 29, 29, 29, 52, 52, 201, 201, 201, 201, 29, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 44, 45, 46, 47, 48, 49, 50, 51, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086602 none CC1(CNN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.2', 'O.co2', 'O.co2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 186, 73, 42, 42, 15, 15, 15, 15, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 15, 201, 201, 201, 201, 201, 201, 201, 185, 185, 74, 42, 15, 16, 16, 8, 8, 1, 1, 1, 1, 15, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 778 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086602 none CC1(CNN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.2', 'O.co2', 'O.co2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 15, 15, 15, 15, 16, 16, 16, 15, 1, 29, 29, 29, 29, 29, 29, 29, 24, 24, 10, 5, 1, 1, 1, 2, 2, 15, 15, 15, 15, 1, 29, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 43, 22] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086602 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086602 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086602/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086602 Building REAL300000086603 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086603' /scratch/stefan/7769667/working/building/REAL300000086603 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086603 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086603/0 /scratch/stefan/7769667/working/building/REAL300000086603 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/629 `/scratch/stefan/7769667/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNCC2(C)CCCC2)C(OCC(=O)[O-])=C1) `REAL300000086603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086603 none COC1=CC=C(C=NNCC2(C)CCCC2)C(OCC(=O)[O-])=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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 12, 5, 1, 11, 11, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 11, 35, 69, 69, 69, 69, 69, 1, 1, 7, 38, 58, 58, 1, 3, 3, 3, 1, 1, 4, 11, 35, 35, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 38, 38, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 45, 16, 17, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 431 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086603 none COC1=CC=C(C=NNCC2(C)CCCC2)C(OCC(=O)[O-])=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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 12, 5, 1, 11, 11, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 69, 48, 69, 69, 47, 47, 16, 5, 1, 1, 1, 1, 1, 1, 1, 69, 69, 146, 199, 201, 201, 69, 80, 80, 80, 69, 69, 47, 16, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 199, 199, 69] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45]) total number of confs: 658 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086603 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086603 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086603/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086603 Building REAL300000086604 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086604' /scratch/stefan/7769667/working/building/REAL300000086604 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086604 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086604/0 /scratch/stefan/7769667/working/building/REAL300000086604 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/630 `/scratch/stefan/7769667/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)CCCC1) `REAL300000086604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086604 none CC1(CNN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 4, 13, 26, 26, 34, 34, 26, 34, 118, 201, 201, 201, 201, 201, 34, 34, 1, 1, 1, 1, 2, 2, 2, 4, 4, 13, 26, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 34, 19, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 610 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086604 none CC1(CNN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 7, 4, 4, 1, 1, 1, 1, 1, 1, 11, 36, 35, 35, 52, 52, 1, 1, 34, 34, 34, 34, 34, 34, 34, 19, 19, 7, 4, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086604 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086604 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086604/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086604 Building REAL300000086605 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086605' /scratch/stefan/7769667/working/building/REAL300000086605 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086605 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086605/0 /scratch/stefan/7769667/working/building/REAL300000086605 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/631 `/scratch/stefan/7769667/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NNCC1(C)CCCC1) `REAL300000086605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086605 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNCC1(C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 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, 2, 2, 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, 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, 2, 2, 1, 1, 1, 1, 1, 13, 13, 44, 81, 120, 120, 120, 120, 120, 2, 2, 2, 1, 13, 44, 81, 81, 120, 120, 120, 120, 120, 120, 120, 120, 120, 120, 120] 120 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 23] set([4, 5, 11, 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]) total number of confs: 415 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086605 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNCC1(C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 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, 2, 2, 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, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 120, 120, 120, 120, 120, 72, 72, 25, 10, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 72, 25, 10, 10, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 120 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 226 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086605 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086605 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086605/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086605 Building REAL300000086606 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086606' /scratch/stefan/7769667/working/building/REAL300000086606 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086606 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086606/0 /scratch/stefan/7769667/working/building/REAL300000086606 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/632 `/scratch/stefan/7769667/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)CCCC1) `REAL300000086606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086606 none CC1(CNN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 6, 17, 39, 39, 94, 94, 64, 94, 167, 201, 201, 201, 94, 94, 94, 1, 1, 1, 1, 2, 2, 2, 6, 6, 17, 39, 94, 94, 201, 201, 94, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 34, 18, 19, 20, 21] set([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]) total number of confs: 597 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086606 none CC1(CNN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 56, 18, 7, 7, 1, 1, 1, 1, 1, 1, 7, 29, 41, 41, 1, 1, 1, 94, 94, 94, 94, 94, 94, 94, 56, 56, 18, 7, 1, 1, 29, 29, 1, 94, 94, 94, 94, 94, 94, 94, 94] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 15, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 468 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086606 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086606 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086606/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086606 Building REAL300000086607 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086607' /scratch/stefan/7769667/working/building/REAL300000086607 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086607 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086607/0 /scratch/stefan/7769667/working/building/REAL300000086607 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/633 `/scratch/stefan/7769667/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNCC2(C)CCCC2)C=C1) `REAL300000086607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086607 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNCC2(C)CCCC2)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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 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, 3, 7, 7, 3, 7, 7, 2, 2, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 11, 34, 84, 165, 165, 165, 165, 165, 1, 1, 3, 3, 3, 1, 11, 34, 84, 84, 165, 165, 165, 165, 165, 165, 165, 165, 165, 165, 165, 1, 1] 165 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 44, 43, 22, 23, 27] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 539 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086607 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNCC2(C)CCCC2)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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 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, 3, 7, 7, 3, 7, 7, 2, 2, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 165, 165, 165, 165, 165, 165, 165, 108, 108, 32, 9, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 165, 108, 32, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 165, 165] 165 rigid atoms, others: [35, 36, 37, 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, 43, 44]) total number of confs: 301 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086607 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086607 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086607/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086607 Building REAL300000086608 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086608' /scratch/stefan/7769667/working/building/REAL300000086608 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086608 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086608/0 /scratch/stefan/7769667/working/building/REAL300000086608 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/634 `/scratch/stefan/7769667/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)CCCC1) `REAL300000086608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086608 none CC1(CNN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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, 10, 31, 69, 69, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 2, 2, 2, 10, 10, 31, 69, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 1, 1] 76 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 40, 39, 34, 18, 19, 20, 21] set([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]) total number of confs: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086608 none CC1(CNN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 51, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 76, 76, 52, 52, 17, 4, 1, 1, 1, 1, 76, 76, 76, 76, 76, 76, 76, 76] 76 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 276 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086608 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086608/1 /scratch/stefan/7769667/working/building/REAL300000086608 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/635 `/scratch/stefan/7769667/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)CCCC1) `REAL300000086608.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086608 none CC1(CNN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 10, 29, 85, 85, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 1, 1, 1, 1, 2, 2, 2, 10, 10, 29, 85, 131, 131, 131, 131, 1, 1, 1, 1, 1, 1, 1, 1] 131 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 40, 39, 34, 18, 19, 20, 21] set([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]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086608 none CC1(CNN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 89, 40, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 131, 131, 131, 131, 131, 131, 131, 89, 89, 40, 11, 1, 1, 1, 1, 131, 131, 131, 131, 131, 131, 131, 131] 131 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 454 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086608 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086608 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086608/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086608/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086608 Building REAL300000086609 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086609' /scratch/stefan/7769667/working/building/REAL300000086609 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086609 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086609/0 /scratch/stefan/7769667/working/building/REAL300000086609 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/636 `/scratch/stefan/7769667/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC2(C)CCCC2)=C([N+](=O)[O-])C=C1OCC(=O)[O-]) `REAL300000086609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086609 none COC1=CC(C=NNCC2(C)CCCC2)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [4, 1, 1, 1, 1, 1, 5, 5, 12, 40, 72, 72, 72, 72, 72, 1, 1, 2, 2, 1, 1, 1, 8, 16, 22, 22, 4, 4, 4, 1, 5, 12, 40, 40, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 1, 16, 16] 201 rigid atoms, others: [1, 2, 3, 4, 5, 45, 15, 16, 19, 20, 21, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 335 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086609 none COC1=CC(C=NNCC2(C)CCCC2)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [111, 72, 72, 72, 35, 35, 14, 5, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 72, 72, 187, 201, 201, 201, 111, 111, 111, 72, 35, 14, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201] 201 rigid atoms, others: [43, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47]) total number of confs: 455 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086609 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086609 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086609/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086609 Building REAL300000086610 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086610' /scratch/stefan/7769667/working/building/REAL300000086610 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086610 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086610/0 /scratch/stefan/7769667/working/building/REAL300000086610 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/637 `/scratch/stefan/7769667/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNCC1(C)CCCC1) `REAL300000086610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086610 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNCC1(C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 13, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 23, 75, 143, 143, 143, 143, 143, 4, 4, 4, 13, 13, 1, 1, 1, 4, 23, 75, 75, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143] 201 rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 560 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086610 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNCC1(C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 143, 173, 201, 201, 201, 143, 143, 143, 143, 143, 143, 143, 143, 143, 105, 105, 29, 9, 1, 1, 1, 1, 1, 1, 1, 173, 173, 173, 201, 201, 143, 143, 143, 105, 29, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 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: 535 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086610 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086610 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086610/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086610 Building REAL300000086611 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086611' /scratch/stefan/7769667/working/building/REAL300000086611 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086611 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086611/0 /scratch/stefan/7769667/working/building/REAL300000086611 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/638 `/scratch/stefan/7769667/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC2(C)CCCC2)=CC=C1OCCC(=O)[O-]) `REAL300000086611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086611 none COC1=CC(C=NNCC2(C)CCCC2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 15, 39, 64, 64, 64, 64, 64, 1, 1, 1, 1, 9, 18, 18, 30, 28, 3, 3, 3, 1, 7, 15, 39, 39, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 18, 18, 18, 18] 201 rigid atoms, others: [1, 2, 3, 4, 5, 43, 44, 15, 16, 17, 18, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086611 none COC1=CC(C=NNCC2(C)CCCC2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 64, 64, 64, 27, 27, 12, 3, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 145, 191, 191, 201, 186, 96, 96, 96, 64, 27, 12, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 64, 64, 191, 191, 191, 191] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48]) total number of confs: 577 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086611 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086611 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086611/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086611 Building REAL300000086612 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086612' /scratch/stefan/7769667/working/building/REAL300000086612 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086612 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086612/0 /scratch/stefan/7769667/working/building/REAL300000086612 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/639 `/scratch/stefan/7769667/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=NNCC2(C)CCCC2)C=C1)C(=O)[O-]) `REAL300000086612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086612 none CC(OC1=CC=C(C=NNCC2(C)CCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 6, 6, 16, 51, 98, 98, 98, 98, 98, 1, 1, 14, 20, 20, 14, 14, 14, 14, 1, 1, 6, 16, 51, 51, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 43, 44, 17, 18, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 403 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086612 none CC(OC1=CC=C(C=NNCC2(C)CCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 151, 98, 67, 98, 98, 38, 38, 15, 5, 1, 1, 1, 1, 1, 1, 1, 98, 98, 201, 201, 201, 201, 201, 201, 201, 98, 98, 38, 15, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 98, 98] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44]) total number of confs: 696 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086612 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086612 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086612/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086612 Building REAL300000086613 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086613' /scratch/stefan/7769667/working/building/REAL300000086613 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086613 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086613/0 /scratch/stefan/7769667/working/building/REAL300000086613 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/640 `/scratch/stefan/7769667/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)CCCC1) `REAL300000086613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086613 none CC1(CNN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 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, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 7, 18, 61, 61, 124, 124, 124, 201, 201, 201, 124, 124, 124, 124, 124, 124, 1, 1, 1, 1, 2, 2, 2, 7, 7, 18, 61, 124, 201, 201, 124, 124, 124, 124, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 602 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086613 none CC1(CNN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 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, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 70, 25, 7, 7, 1, 1, 1, 1, 1, 8, 14, 14, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 124, 124, 124, 70, 70, 25, 7, 1, 8, 8, 1, 1, 1, 1, 124, 124, 124, 124, 124, 124, 124, 124] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 475 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086613 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086613 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086613/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086613 Building REAL300000086614 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086614' /scratch/stefan/7769667/working/building/REAL300000086614 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086614 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086614/0 /scratch/stefan/7769667/working/building/REAL300000086614 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/641 `/scratch/stefan/7769667/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC1(C)CCCC1)C1=CC=CC(OCCCC(=O)[O-])=C1) `REAL300000086614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086614 none CC(=NNCC1(C)CCCC1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 2, 1, 1, 1, 1, 1, 1, 1, 10, 28, 28, 28, 28, 28, 67, 118, 139, 201, 201, 201, 28, 10, 10, 10, 7, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 118, 118, 139, 139, 201, 201, 28] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 36, 38, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 787 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086614 none CC(=NNCC1(C)CCCC1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 13, 22, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 6, 18, 29, 46, 60, 60, 1, 9, 9, 9, 13, 22, 22, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 18, 18, 28, 28, 46, 46, 1] 201 rigid atoms, others: [1, 43, 41, 42, 11, 12, 13, 14, 15, 16, 50, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48, 49]) total number of confs: 344 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086614 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086614 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086614/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086614 Building REAL300000086615 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086615' /scratch/stefan/7769667/working/building/REAL300000086615 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086615 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086615/0 /scratch/stefan/7769667/working/building/REAL300000086615 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/642 `/scratch/stefan/7769667/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NCC1(C)CCCC1) `REAL300000086615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086615 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NCC1(C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', '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', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 1, 1, 9, 19, 19, 24, 24, 1, 1, 4, 12, 12, 38, 75, 75, 75, 75, 75, 4, 4, 4, 4, 2, 2, 2, 2, 1, 1, 19, 19, 19, 19, 1, 1, 38, 38, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 39, 14, 15, 40] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 326 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086615 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NCC1(C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', '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', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 57, 75, 75, 75, 75, 75, 75, 186, 201, 201, 201, 201, 75, 75, 17, 4, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 75, 75, 75, 75, 75, 75, 201, 201, 201, 201, 75, 75, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [51, 50, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 52, 53] 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, 40, 41, 42, 43, 44, 45]) total number of confs: 550 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086615 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086615 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086615/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086615 Building REAL300000086616 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086616' /scratch/stefan/7769667/working/building/REAL300000086616 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086616 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086616/0 /scratch/stefan/7769667/working/building/REAL300000086616 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/643 `/scratch/stefan/7769667/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NCC1(C)CCCC1) `REAL300000086616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086616 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NCC1(C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 1, 1, 6, 14, 28, 28, 1, 1, 4, 14, 14, 46, 81, 81, 81, 81, 81, 4, 4, 4, 4, 2, 2, 2, 2, 1, 1, 14, 14, 1, 1, 46, 46, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 13, 14, 36, 37] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086616 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NCC1(C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 61, 81, 81, 81, 81, 81, 81, 180, 201, 201, 201, 81, 81, 17, 4, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 81, 81, 81, 81, 81, 81, 201, 201, 81, 81, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [50, 49, 43, 44, 45, 46, 47, 48, 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, 37, 38, 39, 40, 41, 42]) total number of confs: 601 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086616 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086616 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086616/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086616 Building REAL300000086617 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086617' /scratch/stefan/7769667/working/building/REAL300000086617 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086617 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086617/0 /scratch/stefan/7769667/working/building/REAL300000086617 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/644 `/scratch/stefan/7769667/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC1(C)CCCC1)C1=CC=CC(OC(C)C(=O)[O-])=C1) `REAL300000086617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086617 none CC(=NNCC1(C)CCCC1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 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] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 5, 1, 1, 1, 1, 1, 1, 1, 33, 73, 73, 73, 73, 73, 149, 201, 201, 201, 201, 73, 33, 33, 33, 15, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 201, 201, 201, 201, 73] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 36, 38, 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, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 538 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086617 none CC(=NNCC1(C)CCCC1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 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] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 11, 36, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 1, 11, 22, 22, 30, 30, 1, 7, 7, 7, 11, 36, 36, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 1, 22, 22, 22, 22, 1] 201 rigid atoms, others: [1, 40, 41, 42, 11, 12, 13, 14, 15, 16, 22, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46]) total number of confs: 345 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086617 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086617 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086617/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086617 Building REAL300000086618 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086618' /scratch/stefan/7769667/working/building/REAL300000086618 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086618 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086618/0 /scratch/stefan/7769667/working/building/REAL300000086618 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/645 `/scratch/stefan/7769667/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NCC1(C)CCCC1) `REAL300000086618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086618 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NCC1(C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', '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', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 1, 1, 6, 8, 9, 15, 15, 1, 1, 4, 13, 13, 33, 65, 65, 65, 65, 65, 4, 4, 4, 4, 2, 2, 2, 2, 1, 1, 8, 8, 8, 8, 1, 1, 33, 33, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 39, 14, 15, 40] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086618 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NCC1(C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', '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', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 18, 56, 65, 65, 65, 65, 65, 65, 201, 201, 201, 201, 201, 65, 65, 18, 4, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 65, 65, 65, 65, 65, 65, 201, 201, 201, 201, 65, 65, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [51, 50, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 52, 53] 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, 40, 41, 42, 43, 44, 45]) total number of confs: 428 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086618 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086618 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086618/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086618 Building REAL300000086619 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086619' /scratch/stefan/7769667/working/building/REAL300000086619 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086619 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086619/0 /scratch/stefan/7769667/working/building/REAL300000086619 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/646 `/scratch/stefan/7769667/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNCC1(C)CCCC1)C1=CC=C(OCCCCC(=O)[O-])C=C1) `REAL300000086619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086619 none CCC(=NNCC1(C)CCCC1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 10, 4, 1, 1, 1, 1, 1, 1, 1, 24, 58, 58, 24, 24, 112, 138, 175, 175, 189, 189, 189, 58, 58, 34, 34, 34, 34, 34, 10, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 138, 138, 175, 175, 175, 175, 189, 189, 58, 58] 201 rigid atoms, others: [43, 5, 6, 7, 8, 9, 10, 11, 44, 40, 41, 39, 38, 42, 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, 33, 34, 35, 36, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 749 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086619 none CCC(=NNCC1(C)CCCC1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 6, 6, 16, 38, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 6, 8, 22, 22, 29, 33, 35, 1, 1, 9, 9, 9, 9, 9, 16, 38, 38, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 8, 8, 21, 21, 22, 22, 28, 28, 1, 1] 201 rigid atoms, others: [2, 12, 13, 14, 45, 16, 56, 46, 55, 24, 25, 15] set([0, 1, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 373 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086619 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086619 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086619/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086619 Building REAL300000086620 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086620' /scratch/stefan/7769667/working/building/REAL300000086620 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086620 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086620/0 /scratch/stefan/7769667/working/building/REAL300000086620 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/647 `/scratch/stefan/7769667/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=C2CC(C(=O)[O-])(C3=CC=CC=C3)C2)CCCC1) `REAL300000086620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086620 none CC1(CNN=C2CC(C(=O)[O-])(C3=CC=CC=C3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 10, 26, 102, 102, 102, 102, 143, 143, 102, 201, 201, 102, 201, 201, 102, 1, 1, 1, 1, 2, 2, 2, 10, 10, 26, 102, 102, 201, 201, 102, 201, 201, 102, 102, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 41, 42, 43, 44, 18, 19, 20, 21] set([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]) total number of confs: 712 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: REAL300000086620 none CC1(CNN=C2CC(C(=O)[O-])(C3=CC=CC=C3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 114, 45, 7, 7, 7, 7, 1, 7, 12, 12, 1, 1, 1, 1, 1, 1, 7, 201, 201, 201, 201, 201, 201, 201, 114, 114, 45, 7, 7, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 7, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 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: 715 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086620 none CC1(CNN=C2CC(C(=O)[O-])(C3=CC=CC=C3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 42, 11, 1, 1, 1, 1, 1, 1, 3, 3, 1, 7, 7, 1, 7, 7, 1, 102, 102, 102, 102, 102, 102, 102, 42, 42, 11, 1, 1, 7, 7, 1, 7, 7, 1, 1, 102, 102, 102, 102, 102, 102, 102, 102] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 17, 35, 36, 28, 29] set([0, 1, 2, 9, 10, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 344 number of broken/clashed sets: 175 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086620 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086620 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086620/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086620 Building REAL300000086621 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086621' /scratch/stefan/7769667/working/building/REAL300000086621 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086621 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086621/0 /scratch/stefan/7769667/working/building/REAL300000086621 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/648 `/scratch/stefan/7769667/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNCC2(C)CCCC2)=CC=C1OCCCC(=O)[O-]) `REAL300000086621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086621 none COC1=CC(C(C)=NNCC2(C)CCCC2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 21, 44, 67, 67, 67, 67, 67, 1, 1, 1, 1, 7, 14, 16, 24, 30, 30, 3, 3, 3, 1, 7, 7, 7, 21, 44, 44, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 14, 14, 16, 16, 24, 24] 201 rigid atoms, others: [1, 2, 3, 4, 5, 48, 47, 16, 17, 18, 19, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53, 54]) total number of confs: 369 number of broken/clashed sets: 170 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086621 none COC1=CC(C(C)=NNCC2(C)CCCC2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 67, 67, 67, 26, 26, 26, 10, 3, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 131, 191, 195, 201, 201, 201, 103, 103, 103, 67, 26, 26, 26, 10, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 191, 191, 195, 195, 201, 201] 201 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 645 number of broken/clashed sets: 170 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086621 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086621 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086621/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086621 Building REAL300000086622 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086622' /scratch/stefan/7769667/working/building/REAL300000086622 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086622 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086622/0 /scratch/stefan/7769667/working/building/REAL300000086622 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/649 `/scratch/stefan/7769667/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC1(C)CCCC1)C1=CC(Br)=CC=C1OCC(=O)[O-]) `REAL300000086622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086622 none CC(=NNCC1(C)CCCC1)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 14, 4, 1, 1, 1, 1, 1, 1, 1, 43, 80, 80, 80, 43, 80, 80, 80, 165, 201, 201, 201, 43, 43, 43, 14, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 36, 38, 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, 40, 41, 42, 43, 44]) total number of confs: 665 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086622 none CC(=NNCC1(C)CCCC1)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 14, 39, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 1, 1, 7, 29, 49, 49, 6, 6, 6, 14, 39, 39, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 1, 1, 1, 29, 29] 201 rigid atoms, others: [1, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44]) total number of confs: 434 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086622 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086622 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086622/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086622 Building REAL300000086623 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086623' /scratch/stefan/7769667/working/building/REAL300000086623 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086623 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086623/0 /scratch/stefan/7769667/working/building/REAL300000086623 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/650 `/scratch/stefan/7769667/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNCC1(C)CCCC1)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1) `REAL300000086623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086623 none CC(=NNCC1(C)CCCC1)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [93, 93, 32, 10, 1, 1, 1, 1, 1, 1, 1, 93, 198, 198, 201, 201, 201, 198, 198, 198, 198, 198, 198, 198, 198, 93, 93, 93, 32, 10, 10, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 198, 198, 198, 198, 198, 198] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 41, 36, 38, 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, 33, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 358 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086623 none CC(=NNCC1(C)CCCC1)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [9, 1, 9, 9, 55, 140, 198, 198, 198, 198, 198, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 55, 140, 140, 198, 198, 198, 198, 198, 198, 198, 198, 198, 198, 198, 2, 2, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [1, 49, 44, 11, 12, 13, 45, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 737 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086623 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086623 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086623/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086623 Building REAL300000086624 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086624' /scratch/stefan/7769667/working/building/REAL300000086624 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086624 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086624/0 /scratch/stefan/7769667/working/building/REAL300000086624 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/651 `/scratch/stefan/7769667/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)CCCC1) `REAL300000086624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086624 none CC1(CNN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 4, 11, 24, 24, 37, 37, 37, 37, 37, 112, 199, 201, 201, 199, 201, 201, 199, 201, 201, 37, 1, 1, 1, 1, 2, 2, 2, 4, 4, 11, 24, 37, 37, 37, 199, 201, 201, 199, 201, 201, 37, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 44, 45, 46, 47, 48, 49, 50, 51, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 617 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086624 none CC1(CNN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 175, 94, 63, 63, 41, 41, 41, 41, 41, 8, 3, 1, 3, 4, 4, 1, 1, 1, 1, 1, 1, 41, 201, 201, 201, 201, 201, 201, 201, 175, 175, 94, 63, 41, 41, 41, 3, 1, 1, 1, 1, 1, 41, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 39, 40, 41, 42, 12, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 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: 727 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086624 none CC1(CNN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 30, 37, 37, 30, 41, 41, 30, 41, 41, 1, 37, 37, 37, 37, 37, 37, 37, 22, 22, 8, 4, 1, 1, 1, 30, 41, 41, 30, 41, 41, 1, 37, 37, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 43, 22] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 308 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086624 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086624 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086624/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086624 Building REAL300000086625 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086625' /scratch/stefan/7769667/working/building/REAL300000086625 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086625 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086625/0 /scratch/stefan/7769667/working/building/REAL300000086625 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/652 `/scratch/stefan/7769667/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNCC2(C)CCCC2)=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000086625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086625 none COC1=CC(C=NNCC2(C)CCCC2)=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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 63, 105, 105, 105, 106, 106, 1, 1, 1, 1, 1, 5, 13, 13, 17, 17, 4, 4, 4, 1, 6, 20, 64, 64, 106, 106, 106, 105, 105, 105, 106, 106, 106, 106, 106, 1, 13, 13, 13, 13] 201 rigid atoms, others: [1, 2, 3, 4, 5, 44, 15, 16, 17, 18, 19, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086625 none COC1=CC(C=NNCC2(C)CCCC2)=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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 105, 105, 105, 40, 40, 16, 5, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 188, 200, 200, 201, 201, 157, 157, 157, 105, 40, 16, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 105, 200, 200, 200, 200] 201 rigid atoms, others: [43, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48]) total number of confs: 492 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086625 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086625 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086625/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086625 Building REAL300000086626 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086626' /scratch/stefan/7769667/working/building/REAL300000086626 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086626 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086626/0 /scratch/stefan/7769667/working/building/REAL300000086626 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/653 `/scratch/stefan/7769667/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC(C(=O)[O-])=C(Cl)S2)CCCC1) `REAL300000086626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086626 none CC1(CNN=CC2=CC(C(=O)[O-])=C(Cl)S2)CCCC1 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', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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, 10, 29, 98, 98, 153, 153, 153, 153, 153, 153, 153, 153, 1, 1, 1, 1, 2, 2, 2, 10, 10, 29, 98, 153, 1, 1, 1, 1, 1, 1, 1, 1] 153 rigid atoms, others: [0, 1, 2, 33, 32, 34, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 282 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086626 none CC1(CNN=CC2=CC(C(=O)[O-])=C(Cl)S2)CCCC1 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', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [153, 87, 34, 8, 8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 153, 153, 153, 153, 153, 153, 153, 87, 87, 34, 8, 1, 153, 153, 153, 153, 153, 153, 153, 153] 153 rigid atoms, others: [5, 6, 7, 8, 9, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 505 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086626 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086626 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086626/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086626 Building REAL300000086627 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086627' /scratch/stefan/7769667/working/building/REAL300000086627 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086627 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086627/0 /scratch/stefan/7769667/working/building/REAL300000086627 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/654 `/scratch/stefan/7769667/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)CCCC1) `REAL300000086627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086627 none CC1(CNN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)CCCC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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, 8, 20, 78, 78, 118, 118, 118, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 118, 1, 1, 1, 1, 2, 2, 2, 8, 8, 20, 78, 118, 118, 201, 201, 402, 201, 1, 1, 1, 1, 1, 1, 1, 1] 402 rigid atoms, others: [0, 1, 2, 38, 39, 40, 41, 42, 43, 44, 45, 21, 22, 23, 24] set([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]) total number of confs: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086627 none CC1(CNN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)CCCC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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: [201, 164, 91, 34, 34, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 201, 201, 201, 164, 164, 91, 34, 12, 12, 1, 1, 2, 1, 201, 201, 201, 201, 201, 201, 201, 201] 402 rigid atoms, others: [34, 35, 37, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 719 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086627 none CC1(CNN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)CCCC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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: [118, 58, 20, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 13, 13, 12, 1, 118, 118, 118, 118, 118, 118, 118, 59, 59, 20, 6, 1, 1, 12, 12, 24, 12, 118, 118, 118, 118, 118, 118, 118, 118] 402 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 20] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 432 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086627 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086627 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086627/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086627 Building REAL300000086628 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086628' /scratch/stefan/7769667/working/building/REAL300000086628 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086628 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086628/0 /scratch/stefan/7769667/working/building/REAL300000086628 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/655 `/scratch/stefan/7769667/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNCC1(C)CCCC1) `REAL300000086628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086628 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNCC1(C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 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, 3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 22, 46, 71, 71, 71, 71, 71, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 22, 46, 46, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71] 71 rigid atoms, others: [1, 3, 4, 5, 6, 7, 10, 11, 12, 28, 29, 30] set([0, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 263 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086628 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNCC1(C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 69, 69, 28, 9, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 71, 71, 71, 71, 69, 28, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 71 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 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]) total number of confs: 146 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086628 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086628 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086628/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086628 Building REAL300000086629 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086629' /scratch/stefan/7769667/working/building/REAL300000086629 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086629 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086629/0 /scratch/stefan/7769667/working/building/REAL300000086629 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/656 `/scratch/stefan/7769667/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)CCCC1) `REAL300000086629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086629 none CC1(CNN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)CCCC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 6, 18, 59, 59, 105, 105, 105, 105, 201, 201, 201, 201, 201, 201, 201, 201, 105, 1, 1, 1, 1, 2, 2, 2, 6, 6, 18, 59, 105, 105, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 41, 42, 43, 44, 20, 21, 22, 23] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086629 none CC1(CNN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)CCCC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 154, 88, 44, 44, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 201, 201, 201, 154, 154, 88, 44, 12, 12, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 697 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086629 none CC1(CNN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)CCCC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 57, 21, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 12, 1, 105, 105, 105, 105, 105, 105, 105, 57, 57, 21, 7, 1, 1, 12, 12, 12, 12, 105, 105, 105, 105, 105, 105, 105, 105] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 19, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 377 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086629 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086629 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086629/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086629 Building REAL300000086630 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086630' /scratch/stefan/7769667/working/building/REAL300000086630 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086630 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086630/0 /scratch/stefan/7769667/working/building/REAL300000086630 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/657 `/scratch/stefan/7769667/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)CCCC1) `REAL300000086630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086630 none CC1(CNN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 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, 10, 30, 71, 71, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1, 1, 1, 2, 2, 2, 10, 10, 30, 71, 81, 81, 81, 81, 1, 1, 1, 1, 1, 1, 1, 1] 81 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 40, 39, 34, 18, 19, 20, 21] set([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]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086630 none CC1(CNN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 49, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 81, 49, 49, 21, 5, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 81, 81] 81 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 276 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086630 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086630 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086630/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086630 Building REAL300000086631 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086631' /scratch/stefan/7769667/working/building/REAL300000086631 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086631 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086631/0 /scratch/stefan/7769667/working/building/REAL300000086631 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/658 `/scratch/stefan/7769667/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC(C(=O)[O-])=CC=C2Br)CCCC1) `REAL300000086631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086631 none CC1(CNN=CC2=CC(C(=O)[O-])=CC=C2Br)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 11, 11, 1, 1, 1, 17, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 10, 37, 102, 102, 155, 155, 155, 155, 155, 155, 155, 155, 155, 1, 1, 1, 1, 2, 2, 2, 10, 10, 37, 102, 155, 155, 155, 1, 1, 1, 1, 1, 1, 1, 1] 155 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 34, 16, 17, 18, 19, 37, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 282 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086631 none CC1(CNN=CC2=CC(C(=O)[O-])=CC=C2Br)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 11, 11, 1, 1, 1, 17, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [155, 117, 62, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 155, 155, 117, 117, 62, 12, 1, 1, 1, 155, 155, 155, 155, 155, 155, 155, 155] 155 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 526 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086631 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086631 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086631/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086631 Building REAL300000086632 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086632' /scratch/stefan/7769667/working/building/REAL300000086632 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086632 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086632/0 /scratch/stefan/7769667/working/building/REAL300000086632 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/659 `/scratch/stefan/7769667/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)CCCC1) `REAL300000086632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086632 none CC1(CNN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 264 conformations in input total number of sets (complete confs): 264 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 10, 31, 78, 78, 132, 132, 132, 132, 132, 132, 132, 132, 132, 132, 1, 1, 1, 1, 2, 2, 2, 10, 10, 31, 78, 132, 132, 264, 1, 1, 1, 1, 1, 1, 1, 1] 264 rigid atoms, others: [0, 1, 2, 35, 36, 33, 38, 32, 34, 17, 18, 19, 20, 37, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 510 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086632 none CC1(CNN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 264 conformations in input total number of sets (complete confs): 264 using faster count positions algorithm for large data unique positions, atoms: [132, 92, 40, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 132, 132, 132, 92, 92, 40, 13, 1, 1, 2, 132, 132, 132, 132, 132, 132, 132, 132] 264 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 469 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086632 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086632/1 /scratch/stefan/7769667/working/building/REAL300000086632 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/660 `/scratch/stefan/7769667/working/3D/660' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])CCCC1) `REAL300000086632.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086632 none CC1(CNN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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 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, 10, 30, 68, 68, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 2, 2, 2, 10, 10, 30, 68, 70, 70, 1, 1, 1, 1, 1, 1, 1, 1] 70 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 34, 17, 18, 19, 20, 37, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086632 none CC1(CNN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 47, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70, 70, 47, 47, 18, 5, 1, 1, 70, 70, 70, 70, 70, 70, 70, 70] 70 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 245 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086632 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086632 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086632/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086632/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086632 Building REAL300000086633 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086633' /scratch/stefan/7769667/working/building/REAL300000086633 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086633 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086633/0 /scratch/stefan/7769667/working/building/REAL300000086633 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/661 `/scratch/stefan/7769667/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=CC(C=NNCC2(C)CCCC2)=C1OCC(=O)[O-]) `REAL300000086633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086633 none COC1=CC(Br)=CC(C=NNCC2(C)CCCC2)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 17, 50, 103, 103, 103, 103, 103, 1, 1, 2, 12, 25, 25, 4, 4, 4, 1, 1, 4, 17, 50, 50, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 12, 12] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 426 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086633 none COC1=CC(Br)=CC(C=NNCC2(C)CCCC2)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 103, 103, 103, 103, 103, 103, 70, 70, 21, 7, 1, 1, 1, 1, 1, 1, 1, 103, 103, 149, 201, 201, 201, 154, 154, 154, 103, 103, 70, 21, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45]) total number of confs: 670 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086633 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086633 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086633/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086633 Building REAL300000086634 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086634' /scratch/stefan/7769667/working/building/REAL300000086634 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086634 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086634/0 /scratch/stefan/7769667/working/building/REAL300000086634 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/662 `/scratch/stefan/7769667/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)CCCC1) `REAL300000086634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086634 none CC1(CNN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 5, 5, 5, 5, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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, 8, 21, 62, 62, 74, 74, 62, 62, 119, 123, 201, 201, 201, 201, 201, 201, 201, 74, 74, 1, 1, 1, 1, 2, 2, 2, 8, 8, 21, 62, 74, 74, 123, 123, 201, 201, 74, 74, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 41, 42, 43, 44, 45, 46, 47, 48, 22, 23, 24, 25] set([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, 40]) total number of confs: 433 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: REAL300000086634 none CC1(CNN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 5, 5, 5, 5, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [201, 141, 85, 39, 39, 19, 19, 19, 19, 11, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 201, 201, 201, 201, 201, 201, 201, 141, 141, 85, 39, 19, 19, 9, 9, 1, 1, 19, 19, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 38, 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, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 739 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086634 none CC1(CNN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 5, 5, 5, 5, 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, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [74, 40, 16, 4, 4, 1, 1, 1, 1, 1, 1, 2, 4, 19, 19, 19, 19, 19, 19, 19, 1, 1, 74, 74, 74, 74, 74, 74, 74, 40, 40, 16, 4, 1, 1, 4, 4, 19, 19, 1, 1, 74, 74, 74, 74, 74, 74, 74, 74] 201 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 39, 40, 20, 21] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 279 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086634 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086634 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086634/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086634 Building REAL300000086635 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086635' /scratch/stefan/7769667/working/building/REAL300000086635 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086635 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086635/0 /scratch/stefan/7769667/working/building/REAL300000086635 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/663 `/scratch/stefan/7769667/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC(I)=CC(C(=O)[O-])=C2)CCCC1) `REAL300000086635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086635 none CC1(CNN=CC2=CC(I)=CC(C(=O)[O-])=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 10, 32, 74, 74, 99, 99, 99, 99, 99, 99, 99, 99, 99, 1, 1, 1, 1, 2, 2, 2, 10, 10, 32, 74, 99, 99, 99, 1, 1, 1, 1, 1, 1, 1, 1] 99 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 34, 16, 17, 18, 19, 37, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 202 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086635 none CC1(CNN=CC2=CC(I)=CC(C(=O)[O-])=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 71, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 99, 99, 99, 71, 71, 29, 9, 1, 1, 1, 99, 99, 99, 99, 99, 99, 99, 99] 99 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 351 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086635 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086635 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086635/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086635 Building REAL300000086636 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086636' /scratch/stefan/7769667/working/building/REAL300000086636 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086636 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086636/0 /scratch/stefan/7769667/working/building/REAL300000086636 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/664 `/scratch/stefan/7769667/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)CCCC1) `REAL300000086636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086636 none CC1(CNN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 252 conformations in input total number of sets (complete confs): 252 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 10, 26, 89, 89, 126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 1, 1, 1, 1, 2, 2, 2, 10, 10, 26, 89, 252, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 1, 1, 1] 252 rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 41, 42, 43, 44, 20, 21, 22, 23] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 480 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086636 none CC1(CNN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 252 conformations in input total number of sets (complete confs): 252 using faster count positions algorithm for large data unique positions, atoms: [126, 86, 42, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 126, 126, 126, 86, 86, 41, 10, 2, 1, 1, 1, 1, 1, 126, 126, 126, 126, 126, 126, 126, 126] 252 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 449 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086636 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086636 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086636/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086636 Building REAL300000086637 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086637' /scratch/stefan/7769667/working/building/REAL300000086637 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086637 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086637/0 /scratch/stefan/7769667/working/building/REAL300000086637 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/665 `/scratch/stefan/7769667/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)CCCC1) `REAL300000086637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086637 none CC1(CNN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 6, 17, 42, 42, 46, 46, 42, 46, 121, 121, 121, 121, 121, 201, 201, 201, 121, 46, 46, 1, 1, 1, 1, 2, 2, 2, 6, 6, 17, 42, 46, 46, 121, 121, 121, 201, 201, 121, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 43, 44, 45, 46, 47, 48, 49, 50, 22, 23, 24, 25] set([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, 40, 41, 42]) total number of confs: 706 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086637 none CC1(CNN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 78, 38, 13, 11, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 5, 5, 121, 121, 121, 121, 121, 121, 121, 78, 78, 38, 11, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5, 121, 121, 121, 121, 121, 121, 121, 121] 201 rigid atoms, others: [35, 36, 40, 9, 10, 11, 12, 13, 14, 15, 19, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 461 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086637 none CC1(CNN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 12, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 14, 14, 5, 1, 1, 46, 46, 46, 46, 46, 46, 46, 28, 28, 11, 3, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46] 201 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 20, 21, 41, 42] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086637 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086637 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086637/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086637 Building REAL300000086638 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086638' /scratch/stefan/7769667/working/building/REAL300000086638 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086638 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086638/0 /scratch/stefan/7769667/working/building/REAL300000086638 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/666 `/scratch/stefan/7769667/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=C(C(=O)[O-])C=C(Cl)S2)CCCC1) `REAL300000086638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086638 none CC1(CNN=CC2=C(C(=O)[O-])C=C(Cl)S2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 4, 4, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 7 rigid atoms, others: [0, 1, 2, 33, 32, 34, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086638 none CC1(CNN=CC2=C(C(=O)[O-])C=C(Cl)S2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 16, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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, 4, 2, 2, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 2, 1, 7, 7, 7, 7, 7, 7, 7, 7] 7 rigid atoms, others: [5, 6, 7, 8, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086638 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086638 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086638/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086638 Building REAL300000086639 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086639' /scratch/stefan/7769667/working/building/REAL300000086639 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086639 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086639/0 /scratch/stefan/7769667/working/building/REAL300000086639 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/667 `/scratch/stefan/7769667/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNCC2(C)CCCC2)=CC=C1OCC(=O)[O-]) `REAL300000086639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086639 none CCOC1=CC(C=NNCC2(C)CCCC2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 1, 1, 1, 1, 7, 7, 11, 26, 39, 39, 39, 39, 39, 1, 1, 1, 1, 8, 36, 53, 53, 14, 14, 14, 14, 14, 1, 7, 11, 26, 26, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 36, 36] 201 rigid atoms, others: [2, 3, 4, 5, 6, 45, 46, 16, 17, 18, 19, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086639 none CCOC1=CC(C=NNCC2(C)CCCC2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 5, 1, 11, 11, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 76, 39, 39, 39, 19, 19, 12, 4, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 120, 199, 201, 201, 79, 79, 79, 79, 79, 39, 19, 12, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 199, 199] 201 rigid atoms, others: [43, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 44, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48]) total number of confs: 707 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086639 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086639 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086639/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086639 Building REAL300000086640 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086640' /scratch/stefan/7769667/working/building/REAL300000086640 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086640 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086640/0 /scratch/stefan/7769667/working/building/REAL300000086640 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/668 `/scratch/stefan/7769667/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CN(C3CCOCC3)N=C2C(=O)[O-])CCCC1) `REAL300000086640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086640 none CC1(CNN=CC2=CN(C3CCOCC3)N=C2C(=O)[O-])CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 9, 24, 68, 68, 73, 73, 73, 201, 201, 201, 201, 201, 73, 73, 73, 77, 77, 1, 1, 1, 1, 2, 2, 2, 9, 9, 24, 68, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 41, 42, 43, 44, 45, 46, 47, 48, 20, 21, 22, 23] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 506 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086640 none CC1(CNN=CC2=CN(C3CCOCC3)N=C2C(=O)[O-])CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 144, 77, 28, 28, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 17, 17, 201, 201, 201, 201, 201, 201, 201, 144, 144, 77, 28, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 700 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086640 none CC1(CNN=CC2=CN(C3CCOCC3)N=C2C(=O)[O-])CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 44, 14, 4, 4, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 3, 3, 73, 73, 73, 73, 73, 73, 73, 44, 44, 14, 4, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 73, 73, 73, 73, 73, 73, 73, 73] 201 rigid atoms, others: [5, 6, 7, 8, 9, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086640 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086640 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086640/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086640 Building REAL300000086641 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086641' /scratch/stefan/7769667/working/building/REAL300000086641 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086641 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086641/0 /scratch/stefan/7769667/working/building/REAL300000086641 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/669 `/scratch/stefan/7769667/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C)C(C=NNCC2(C)CCCC2)=C1C(=O)[O-]) `REAL300000086641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086641 none COC1=CC=C(C)C(C=NNCC2(C)CCCC2)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 5, 5, 29, 88, 167, 167, 167, 167, 167, 1, 1, 3, 3, 4, 4, 4, 1, 1, 2, 2, 2, 5, 29, 88, 88, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 579 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086641 none COC1=CC=C(C)C(C=NNCC2(C)CCCC2)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 167, 167, 167, 167, 167, 167, 111, 111, 33, 9, 1, 1, 1, 1, 1, 1, 1, 167, 167, 198, 198, 201, 201, 201, 167, 167, 167, 167, 167, 111, 33, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 498 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086641 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086641 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086641/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086641 Building REAL300000086642 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086642' /scratch/stefan/7769667/working/building/REAL300000086642 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086642 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086642/0 /scratch/stefan/7769667/working/building/REAL300000086642 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/670 `/scratch/stefan/7769667/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C2=CC=C(F)C=C2C(C=NNCC2(C)CCCC2)=C1C(=O)[O-]) `REAL300000086642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086642 none CN1C2=CC=C(F)C=C2C(C=NNCC2(C)CCCC2)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 1, 1, 1, 1, 1, 4, 4, 19, 51, 89, 89, 89, 89, 89, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 4, 19, 51, 51, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89] 89 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086642 none CN1C2=CC=C(F)C=C2C(C=NNCC2(C)CCCC2)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 89, 89, 89, 89, 89, 74, 74, 24, 8, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 74, 24, 8, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 89 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 172 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086642 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086642 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086642/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086642 Building REAL300000086643 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086643' /scratch/stefan/7769667/working/building/REAL300000086643 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086643 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086643/0 /scratch/stefan/7769667/working/building/REAL300000086643 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/671 `/scratch/stefan/7769667/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=C(C(=O)[O-])C=C(Br)S2)CCCC1) `REAL300000086643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086643 none CC1(CNN=CC2=C(C(=O)[O-])C=C(Br)S2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 17, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 4, 4, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 7 rigid atoms, others: [0, 1, 2, 33, 32, 34, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086643 none CC1(CNN=CC2=C(C(=O)[O-])C=C(Br)S2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 17, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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, 4, 2, 2, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 2, 1, 7, 7, 7, 7, 7, 7, 7, 7] 7 rigid atoms, others: [5, 6, 7, 8, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086643 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086643 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086643/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086643 Building REAL300000086644 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086644' /scratch/stefan/7769667/working/building/REAL300000086644 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086644 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086644/0 /scratch/stefan/7769667/working/building/REAL300000086644 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/672 `/scratch/stefan/7769667/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)CCCC1) `REAL300000086644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086644 none CC1(CNN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 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, 9, 23, 76, 76, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 1, 1, 1, 1, 2, 2, 2, 9, 9, 23, 76, 119, 119, 119, 119, 1, 1, 1, 1, 1, 1, 1, 1] 119 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 40, 39, 34, 18, 19, 20, 21] set([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]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086644 none CC1(CNN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 74, 31, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 119, 119, 119, 119, 119, 119, 119, 75, 75, 31, 10, 1, 1, 1, 1, 119, 119, 119, 119, 119, 119, 119, 119] 119 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 405 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086644 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086644 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086644/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086644 Building REAL300000086645 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086645' /scratch/stefan/7769667/working/building/REAL300000086645 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086645 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086645/0 /scratch/stefan/7769667/working/building/REAL300000086645 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/673 `/scratch/stefan/7769667/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)CCCC1) `REAL300000086645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086645 none CC1(CNN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)CCCC1 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', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 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, 10, 28, 69, 69, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 2, 2, 2, 10, 10, 28, 69, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 1, 1] 72 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 40, 39, 34, 18, 19, 20, 21] set([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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086645 none CC1(CNN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)CCCC1 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', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 46, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 72, 72, 46, 46, 18, 5, 1, 1, 1, 1, 72, 72, 72, 72, 72, 72, 72, 72] 72 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086645 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086645 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086645/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086645 Building REAL300000086646 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086646' /scratch/stefan/7769667/working/building/REAL300000086646 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086646 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086646/0 /scratch/stefan/7769667/working/building/REAL300000086646 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/674 `/scratch/stefan/7769667/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)CCCC1) `REAL300000086646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086646 none CC1(CNN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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, 4, 10, 16, 16, 19, 19, 19, 19, 19, 19, 59, 140, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 16, 19, 19, 19, 19, 140, 140, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 41, 42, 43, 44, 45, 46, 47, 48, 22, 23, 24, 25] set([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, 40]) total number of confs: 549 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086646 none CC1(CNN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [201, 183, 92, 81, 81, 79, 79, 79, 79, 79, 79, 40, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 183, 183, 92, 81, 79, 79, 79, 79, 9, 9, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 669 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086646 none CC1(CNN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [19, 13, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 28, 79, 79, 79, 79, 79, 79, 79, 19, 19, 19, 19, 19, 19, 19, 13, 13, 6, 4, 1, 1, 1, 1, 28, 28, 79, 79, 19, 19, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12] 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086646 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086646 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086646/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086646 Building REAL300000086647 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086647' /scratch/stefan/7769667/working/building/REAL300000086647 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086647 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086647/0 /scratch/stefan/7769667/working/building/REAL300000086647 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/675 `/scratch/stefan/7769667/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC=CC(Br)=C2C(=O)[O-])CCCC1) `REAL300000086647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086647 none CC1(CNN=CC2=CC=CC(Br)=C2C(=O)[O-])CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 17, 1, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 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, 9, 21, 42, 42, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 2, 2, 2, 9, 9, 21, 42, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1] 49 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 34, 16, 17, 18, 19, 37, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086647 none CC1(CNN=CC2=CC=CC(Br)=C2C(=O)[O-])CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 17, 1, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 35, 17, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 49, 49, 49, 49, 49, 49, 49, 35, 35, 17, 3, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49] 49 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 4, 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: 169 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086647 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086647 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086647/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086647 Building REAL300000086648 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086648' /scratch/stefan/7769667/working/building/REAL300000086648 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086648 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086648/0 /scratch/stefan/7769667/working/building/REAL300000086648 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/676 `/scratch/stefan/7769667/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=C(C(=O)[O-])C=CC3=C2OCO3)CCCC1) `REAL300000086648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086648 none CC1(CNN=CC2=C(C(=O)[O-])C=CC3=C2OCO3)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 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, 7, 16, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 2, 2, 2, 7, 7, 16, 25, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1] 29 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 40, 39, 34, 18, 19, 20, 21] set([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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086648 none CC1(CNN=CC2=C(C(=O)[O-])C=CC3=C2OCO3)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 14, 4, 4, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 24, 24, 14, 4, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29] 29 rigid atoms, others: [32, 5, 6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086648 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086648 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086648/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086648 Building REAL300000086649 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086649' /scratch/stefan/7769667/working/building/REAL300000086649 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086649 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086649/0 /scratch/stefan/7769667/working/building/REAL300000086649 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/677 `/scratch/stefan/7769667/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)CCCC1) `REAL300000086649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086649 none CC1(CNN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 7, 18, 40, 40, 90, 90, 64, 90, 170, 201, 201, 201, 90, 90, 90, 1, 1, 1, 1, 2, 2, 2, 7, 7, 18, 40, 90, 90, 201, 201, 90, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 34, 18, 19, 20, 21] set([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]) total number of confs: 574 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086649 none CC1(CNN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 51, 18, 7, 7, 1, 1, 1, 1, 1, 1, 7, 24, 36, 36, 1, 1, 1, 90, 90, 90, 90, 90, 90, 90, 51, 51, 18, 7, 1, 1, 24, 24, 1, 90, 90, 90, 90, 90, 90, 90, 90] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 15, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 438 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086649 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086649 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086649/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086649 Building REAL300000086650 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086650' /scratch/stefan/7769667/working/building/REAL300000086650 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086650 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086650/0 /scratch/stefan/7769667/working/building/REAL300000086650 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/678 `/scratch/stefan/7769667/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)CCCC1) `REAL300000086650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086650 none CC1(CNN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 5, 14, 38, 38, 81, 81, 38, 38, 98, 98, 98, 162, 201, 201, 201, 81, 81, 1, 1, 1, 1, 2, 2, 2, 5, 5, 14, 38, 81, 81, 162, 201, 201, 81, 81, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 38, 39, 40, 41, 42, 43, 44, 45, 20, 21, 22, 23] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 1003 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086650 none CC1(CNN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 14, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 28, 40, 40, 1, 1, 81, 81, 81, 81, 81, 81, 81, 39, 39, 14, 4, 1, 1, 9, 28, 28, 1, 1, 81, 81, 81, 81, 81, 81, 81, 81] 201 rigid atoms, others: [32, 36, 5, 6, 7, 8, 9, 10, 18, 19, 37, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 421 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086650 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086650 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086650/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086650 Building REAL300000086651 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086651' /scratch/stefan/7769667/working/building/REAL300000086651 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086651 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086651/0 /scratch/stefan/7769667/working/building/REAL300000086651 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/679 `/scratch/stefan/7769667/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)CCCC1) `REAL300000086651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086651 none CC1(CNN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 11, 11, 14, 1, 1, 1, 1, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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, 9, 24, 82, 82, 149, 149, 149, 149, 149, 149, 149, 149, 149, 149, 149, 149, 1, 1, 1, 1, 2, 2, 2, 9, 9, 24, 82, 149, 149, 149, 1, 1, 1, 1, 1, 1, 1, 1] 149 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 40, 39, 34, 19, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086651 none CC1(CNN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 11, 11, 14, 1, 1, 1, 1, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [149, 104, 49, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 149, 149, 149, 104, 104, 48, 11, 1, 1, 1, 149, 149, 149, 149, 149, 149, 149, 149] 149 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 531 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086651 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086651 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086651/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086651 Building REAL300000086652 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086652' /scratch/stefan/7769667/working/building/REAL300000086652 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086652 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086652/0 /scratch/stefan/7769667/working/building/REAL300000086652 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/680 `/scratch/stefan/7769667/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CNN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)CCCC1) `REAL300000086652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086652 none CC1(CNN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 7, 20, 73, 73, 88, 88, 88, 201, 201, 201, 201, 201, 201, 201, 201, 88, 88, 1, 1, 1, 1, 2, 2, 2, 7, 7, 20, 73, 201, 201, 201, 201, 88, 88, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 41, 42, 43, 44, 20, 21, 22, 23] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 483 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086652 none CC1(CNN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 139, 70, 22, 22, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 201, 201, 201, 201, 201, 201, 201, 139, 139, 70, 22, 1, 1, 1, 1, 12, 12, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 719 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086652 none CC1(CNN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 45, 15, 4, 4, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 22, 22, 12, 1, 1, 88, 88, 88, 88, 88, 88, 88, 45, 45, 15, 4, 12, 12, 12, 12, 1, 1, 88, 88, 88, 88, 88, 88, 88, 88] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 18, 19] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 367 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086652 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086652 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086652/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086652 Building REAL300000086653 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086653' /scratch/stefan/7769667/working/building/REAL300000086653 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086653 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086653/0 /scratch/stefan/7769667/working/building/REAL300000086653 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/681 `/scratch/stefan/7769667/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C=C2)=CC=C1C) `REAL300000086653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086653 none COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 12, 60, 60, 80, 80, 60, 61, 80, 80, 80, 80, 1, 1, 1, 1, 12, 12, 12, 1, 12, 60, 80, 80, 80, 80, 1, 1, 2, 2, 2] 146 rigid atoms, others: [33, 2, 4, 5, 6, 7, 34, 19, 20, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086653 none COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 81, 146, 81, 80, 28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 146, 146, 146, 80, 28, 5, 1, 1, 1, 1, 81, 81, 81, 81, 81] 146 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086653 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086653 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086653/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086653 Building REAL300000086654 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086654' /scratch/stefan/7769667/working/building/REAL300000086654 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086654 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086654/0 /scratch/stefan/7769667/working/building/REAL300000086654 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/682 `/scratch/stefan/7769667/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=CC=C2OCC(=O)[O-])=CC=C1C) `REAL300000086654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086654 none COC(=O)C1=CC(NN=CC2=CC=CC=C2OCC(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', '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.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 10, 1, 1, 1, 1, 7, 12, 12, 19, 19, 12, 19, 19, 19, 58, 111, 117, 117, 1, 1, 1, 1, 10, 10, 10, 1, 7, 12, 19, 19, 19, 19, 111, 111, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 24, 38, 28, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 404 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086654 none COC(=O)C1=CC(NN=CC2=CC=CC=C2OCC(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', '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.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 86, 19, 86, 19, 19, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 48, 48, 19, 19, 19, 19, 86, 86, 86, 19, 8, 4, 1, 1, 1, 1, 27, 27, 19, 19, 19, 19, 19] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 356 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086654 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086654 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086654/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086654 Building REAL300000086655 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086655' /scratch/stefan/7769667/working/building/REAL300000086655 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086655 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086655/0 /scratch/stefan/7769667/working/building/REAL300000086655 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/683 `/scratch/stefan/7769667/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(OCC(=O)[O-])C=C2)=CC=C1C) `REAL300000086655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086655 none COC(=O)C1=CC(NN=CC2=CC=C(OCC(=O)[O-])C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7] 0 hydrogens 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, 6, 12, 13, 18, 18, 13, 16, 59, 99, 119, 119, 18, 18, 1, 1, 1, 1, 9, 9, 9, 1, 6, 12, 18, 18, 99, 99, 18, 18, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 24, 38, 28, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 413 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086655 none COC(=O)C1=CC(NN=CC2=CC=C(OCC(=O)[O-])C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7] 0 hydrogens 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, 18, 79, 18, 18, 7, 4, 4, 1, 1, 1, 1, 1, 1, 6, 18, 31, 31, 1, 1, 18, 18, 18, 18, 79, 79, 79, 18, 7, 4, 1, 1, 18, 18, 1, 1, 18, 18, 18, 18, 18] 201 rigid atoms, others: [32, 35, 36, 9, 10, 11, 12, 13, 14, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086655 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086655 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086655/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086655 Building REAL300000086656 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086656' /scratch/stefan/7769667/working/building/REAL300000086656 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086656 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086656/0 /scratch/stefan/7769667/working/building/REAL300000086656 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/684 `/scratch/stefan/7769667/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=CC(OC(C)C(=O)[O-])=C2)=CC=C1C) `REAL300000086656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086656 none COC(=O)C1=CC(NN=CC2=CC=CC(OC(C)C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 10, 1, 1, 1, 1, 6, 18, 18, 28, 28, 28, 28, 28, 73, 112, 112, 123, 123, 28, 1, 1, 1, 1, 10, 10, 10, 1, 6, 18, 28, 28, 28, 112, 112, 112, 112, 28, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 40, 41, 22, 23, 24, 25, 29] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 389 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086656 none COC(=O)C1=CC(NN=CC2=CC=CC(OC(C)C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 28, 106, 28, 28, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 25, 25, 1, 28, 28, 28, 28, 106, 106, 106, 28, 8, 4, 1, 1, 1, 21, 21, 21, 21, 1, 28, 28, 29, 29, 29] 201 rigid atoms, others: [32, 33, 34, 39, 9, 10, 11, 12, 13, 14, 15, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 341 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086656 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086656 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086656/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086656 Building REAL300000086657 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086657' /scratch/stefan/7769667/working/building/REAL300000086657 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086657 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086657/0 /scratch/stefan/7769667/working/building/REAL300000086657 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/685 `/scratch/stefan/7769667/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=CC(OCCC(=O)[O-])=C2)=CC=C1C) `REAL300000086657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086657 none COC(=O)C1=CC(NN=CC2=CC=CC(OCCC(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 14, 14, 23, 23, 23, 23, 23, 81, 93, 93, 134, 134, 23, 1, 1, 1, 1, 11, 11, 11, 1, 6, 14, 23, 23, 23, 93, 93, 93, 93, 23, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 40, 41, 22, 23, 24, 25, 29] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 367 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086657 none COC(=O)C1=CC(NN=CC2=CC=CC(OCCC(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 99, 23, 99, 23, 23, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 25, 25, 1, 23, 23, 23, 23, 99, 99, 99, 23, 9, 4, 1, 1, 1, 15, 15, 15, 15, 1, 23, 23, 24, 24, 24] 201 rigid atoms, others: [32, 33, 34, 39, 9, 10, 11, 12, 13, 14, 15, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 314 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086657 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086657 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086657/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086657 Building REAL300000086658 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086658' /scratch/stefan/7769667/working/building/REAL300000086658 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086658 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086658/0 /scratch/stefan/7769667/working/building/REAL300000086658 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/686 `/scratch/stefan/7769667/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)=CC=C1C) `REAL300000086658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086658 none COC(=O)C1=CC(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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] 0 hydrogens 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, 1, 6, 14, 15, 21, 21, 15, 15, 57, 117, 127, 127, 21, 21, 21, 21, 21, 1, 1, 1, 1, 12, 12, 12, 1, 6, 14, 21, 21, 117, 117, 21, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 40, 39, 24, 25, 26, 27, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 474 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086658 none COC(=O)C1=CC(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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] 0 hydrogens 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, 107, 21, 107, 21, 21, 8, 4, 4, 1, 1, 1, 1, 1, 1, 7, 17, 23, 23, 1, 1, 2, 2, 1, 21, 21, 21, 21, 107, 107, 107, 21, 8, 4, 1, 1, 17, 17, 1, 21, 21, 21, 21, 21] 201 rigid atoms, others: [34, 35, 38, 9, 10, 11, 12, 13, 14, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086658 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086658 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086658/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086658 Building REAL300000086659 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086659' /scratch/stefan/7769667/working/building/REAL300000086659 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086659 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086659/0 /scratch/stefan/7769667/working/building/REAL300000086659 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/687 `/scratch/stefan/7769667/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=CC(OCC(=O)[O-])=C2)=CC=C1C) `REAL300000086659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086659 none COC(=O)C1=CC(NN=CC2=CC=CC(OCC(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 16, 16, 23, 23, 23, 23, 23, 67, 101, 113, 113, 23, 1, 1, 1, 1, 11, 11, 11, 1, 6, 16, 23, 23, 23, 101, 101, 23, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 24, 38, 28, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 344 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086659 none COC(=O)C1=CC(NN=CC2=CC=CC(OCC(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 23, 84, 23, 23, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 20, 29, 29, 1, 23, 23, 23, 23, 84, 84, 84, 23, 7, 3, 1, 1, 1, 20, 20, 1, 23, 23, 24, 24, 24] 201 rigid atoms, others: [32, 33, 36, 9, 10, 11, 12, 13, 14, 15, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 293 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086659 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086659 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086659/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086659 Building REAL300000086660 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086660' /scratch/stefan/7769667/working/building/REAL300000086660 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086660 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086660/0 /scratch/stefan/7769667/working/building/REAL300000086660 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/688 `/scratch/stefan/7769667/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(OC)C=C2OCC(=O)[O-])=CC=C1C) `REAL300000086660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086660 none COC(=O)C1=CC(NN=CC2=CC=C(OC)C=C2OCC(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 7] 0 hydrogens 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, 7, 15, 15, 21, 21, 15, 21, 26, 21, 21, 21, 54, 123, 129, 129, 1, 1, 1, 1, 11, 11, 11, 1, 7, 15, 21, 21, 26, 26, 26, 21, 123, 123, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 41, 42, 23, 24, 25, 26, 30] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 475 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086660 none COC(=O)C1=CC(NN=CC2=CC=C(OC)C=C2OCC(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 7] 0 hydrogens 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, 96, 21, 96, 21, 21, 8, 4, 4, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 8, 30, 48, 48, 21, 21, 21, 21, 96, 96, 96, 21, 8, 4, 1, 1, 3, 3, 3, 1, 30, 30, 21, 21, 21, 21, 21] 201 rigid atoms, others: [33, 34, 38, 9, 10, 11, 12, 13, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 393 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086660 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086660 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086660/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086660 Building REAL300000086661 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086661' /scratch/stefan/7769667/working/building/REAL300000086661 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086661 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086661/0 /scratch/stefan/7769667/working/building/REAL300000086661 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/689 `/scratch/stefan/7769667/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=CC=C1C) `REAL300000086661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086661 none COC(=O)C1=CC(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 10, 10, 14, 14, 10, 14, 56, 110, 110, 110, 132, 132, 14, 14, 1, 1, 1, 1, 12, 12, 12, 1, 6, 10, 14, 14, 14, 14, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 23, 24, 25, 26, 38, 30, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 459 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086661 none COC(=O)C1=CC(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 52, 15, 14, 7, 3, 3, 1, 1, 1, 1, 1, 1, 9, 29, 29, 29, 46, 46, 1, 1, 15, 15, 15, 15, 52, 52, 52, 14, 7, 3, 1, 1, 1, 1, 15, 15, 15, 15, 15] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086661 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086661 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086661/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086661 Building REAL300000086662 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086662' /scratch/stefan/7769667/working/building/REAL300000086662 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086662 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086662/0 /scratch/stefan/7769667/working/building/REAL300000086662 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/690 `/scratch/stefan/7769667/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)=CC=C1C) `REAL300000086662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086662 none COC(=O)C1=CC(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 10, 47, 48, 105, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1, 1, 12, 12, 12, 1, 10, 47, 105, 105, 105, 105, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 35, 4, 5, 6, 7, 34, 20, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086662 none COC(=O)C1=CC(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 105, 201, 105, 105, 37, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 201, 201, 201, 105, 37, 10, 1, 2, 2, 2, 105, 105, 105, 105, 105] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 504 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086662 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086662 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086662/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086662 Building REAL300000086663 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086663' /scratch/stefan/7769667/working/building/REAL300000086663 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086663 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086663/0 /scratch/stefan/7769667/working/building/REAL300000086663 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/691 `/scratch/stefan/7769667/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)=CC=C1C) `REAL300000086663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086663 none COC(=O)C1=CC(NN=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 1, 11, 1, 1, 1, 1, 4, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 12, 12, 1, 1, 1, 1, 11, 11, 11, 1, 4, 6, 12, 19, 19, 19, 12, 12, 1, 1, 2, 2, 2] 31 rigid atoms, others: [2, 4, 5, 6, 7, 40, 41, 24, 25, 26, 27, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086663 none COC(=O)C1=CC(NN=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 12, 31, 12, 12, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 12, 12, 12, 12, 31, 31, 31, 12, 7, 5, 1, 3, 3, 3, 1, 1, 12, 12, 12, 12, 12] 31 rigid atoms, others: [34, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086663 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086663 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086663/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086663 Building REAL300000086664 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086664' /scratch/stefan/7769667/working/building/REAL300000086664 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086664 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086664/0 /scratch/stefan/7769667/working/building/REAL300000086664 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/692 `/scratch/stefan/7769667/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)=CC=C1C) `REAL300000086664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086664 none COC(=O)C1=CC(NN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 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: [13, 13, 1, 13, 1, 1, 1, 1, 10, 50, 50, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 13, 13, 13, 1, 10, 50, 72, 72, 72, 72, 1, 1, 2, 2, 2] 144 rigid atoms, others: [2, 4, 5, 6, 7, 25, 22, 23, 24, 36, 29, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086664 none COC(=O)C1=CC(NN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 72, 144, 72, 72, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 144, 144, 144, 72, 31, 8, 1, 1, 1, 1, 72, 72, 72, 72, 72] 144 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 369 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086664 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086664/1 /scratch/stefan/7769667/working/building/REAL300000086664 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/693 `/scratch/stefan/7769667/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)=CC=C1C) `REAL300000086664.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086664 none COC(=O)C1=CC(NN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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, 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: [10, 10, 1, 10, 1, 1, 1, 1, 6, 21, 21, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 10, 10, 10, 1, 6, 21, 33, 33, 33, 33, 1, 1, 2, 2, 2] 68 rigid atoms, others: [2, 4, 5, 6, 7, 25, 22, 23, 24, 36, 29, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086664 none COC(=O)C1=CC(NN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 33, 68, 33, 33, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 33, 33, 33, 33, 68, 68, 68, 33, 20, 6, 1, 1, 1, 1, 33, 33, 33, 33, 33] 68 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 189 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086664 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086664 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086664/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086664/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086664 Building REAL300000086665 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086665' /scratch/stefan/7769667/working/building/REAL300000086665 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086665 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086665/0 /scratch/stefan/7769667/working/building/REAL300000086665 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/694 `/scratch/stefan/7769667/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CN(CC(=O)[O-])N=N2)=CC=C1C) `REAL300000086665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086665 none COC(=O)C1=CC(NN=CC2=CN(CC(=O)[O-])N=N2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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] 0 hydrogens 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, 6, 22, 22, 51, 51, 51, 106, 112, 112, 51, 51, 1, 1, 1, 1, 13, 13, 13, 1, 6, 22, 51, 106, 106, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 19, 20, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 397 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086665 none COC(=O)C1=CC(NN=CC2=CN(CC(=O)[O-])N=N2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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] 0 hydrogens 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, 51, 156, 51, 51, 19, 7, 7, 1, 1, 1, 1, 1, 6, 12, 12, 1, 1, 51, 51, 51, 51, 156, 156, 156, 51, 18, 7, 1, 6, 6, 51, 51, 51, 51, 51] 201 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 423 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086665 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086665/1 /scratch/stefan/7769667/working/building/REAL300000086665 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/695 `/scratch/stefan/7769667/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(N=NCC2=CN(CC(=O)[O-])N=N2)=CC=C1C) `REAL300000086665.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086665 none COC(=O)C1=CC(N=NCC2=CN(CC(=O)[O-])N=N2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 5, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens 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, 2, 2, 14, 67, 67, 67, 102, 104, 104, 67, 67, 1, 1, 1, 1, 9, 9, 9, 1, 14, 14, 67, 102, 102, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 19, 20, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 353 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086665 none COC(=O)C1=CC(N=NCC2=CN(CC(=O)[O-])N=N2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 5, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [181, 181, 67, 181, 67, 67, 39, 39, 9, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 67, 67, 67, 67, 181, 181, 181, 67, 9, 9, 1, 3, 3, 67, 67, 67, 67, 67] 201 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 460 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086665 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086665 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086665/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086665/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086665 Building REAL300000086666 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086666' /scratch/stefan/7769667/working/building/REAL300000086666 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086666 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086666/0 /scratch/stefan/7769667/working/building/REAL300000086666 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/696 `/scratch/stefan/7769667/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(OCCC(=O)[O-])C(OC)=C2)=CC=C1C) `REAL300000086666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086666 none COC(=O)C1=CC(NN=CC2=CC=C(OCCC(=O)[O-])C(OC)=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'O.3', 'C.3', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 8, 8, 22, 22, 22, 22, 62, 96, 96, 141, 127, 22, 22, 34, 22, 1, 1, 1, 1, 9, 9, 9, 1, 4, 8, 22, 22, 96, 96, 96, 96, 34, 34, 34, 22, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 44, 45, 24, 25, 26, 27, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 480 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086666 none COC(=O)C1=CC(NN=CC2=CC=C(OCCC(=O)[O-])C(OC)=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'O.3', 'C.3', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 68, 22, 68, 22, 22, 11, 7, 7, 1, 1, 1, 1, 1, 1, 9, 16, 16, 27, 25, 1, 1, 3, 1, 22, 22, 22, 22, 68, 68, 68, 22, 11, 7, 1, 1, 16, 16, 16, 16, 3, 3, 3, 1, 22, 22, 22, 22, 22] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 43, 20, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086666 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086666 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086666/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086666 Building REAL300000086667 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086667' /scratch/stefan/7769667/working/building/REAL300000086667 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086667 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086667/0 /scratch/stefan/7769667/working/building/REAL300000086667 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/697 `/scratch/stefan/7769667/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C=C2Cl)=CC=C1C) `REAL300000086667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086667 none COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C=C2Cl)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 8, 38, 39, 67, 67, 39, 47, 67, 67, 67, 67, 67, 1, 1, 1, 1, 12, 12, 12, 1, 8, 38, 67, 67, 67, 1, 1, 2, 2, 2] 107 rigid atoms, others: [33, 2, 4, 5, 6, 7, 34, 20, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086667 none COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C=C2Cl)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 67, 107, 67, 67, 33, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 67, 67, 67, 67, 107, 107, 107, 67, 33, 9, 1, 1, 1, 67, 67, 67, 67, 67] 107 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 253 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086667 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086667 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086667/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086667 Building REAL300000086668 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086668' /scratch/stefan/7769667/working/building/REAL300000086668 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086668 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086668/0 /scratch/stefan/7769667/working/building/REAL300000086668 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/698 `/scratch/stefan/7769667/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)=CC=C1C) `REAL300000086668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086668 none COC(=O)C1=CC(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [13, 13, 1, 13, 1, 1, 1, 1, 4, 13, 13, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 13, 13, 13, 1, 4, 13, 32, 32, 64, 32, 1, 1, 2, 2, 2] 106 rigid atoms, others: [2, 35, 4, 5, 6, 7, 34, 20, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086668 none COC(=O)C1=CC(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [53, 53, 32, 53, 32, 32, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 32, 32, 32, 32, 53, 53, 53, 32, 22, 6, 1, 1, 2, 1, 32, 32, 32, 32, 32] 106 rigid atoms, others: [33, 9, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 34, 35, 36, 37, 38]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086668 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086668 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086668/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086668 Building REAL300000086669 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086669' /scratch/stefan/7769667/working/building/REAL300000086669 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086669 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086669/0 /scratch/stefan/7769667/working/building/REAL300000086669 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/699 `/scratch/stefan/7769667/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(OC(C)C(=O)[O-])C=C2)=CC=C1C) `REAL300000086669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086669 none COC(=O)C1=CC(NN=CC2=CC=C(OC(C)C(=O)[O-])C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 10, 1, 1, 1, 1, 6, 14, 14, 25, 25, 15, 15, 68, 117, 117, 133, 134, 25, 25, 1, 1, 1, 1, 10, 10, 10, 1, 6, 14, 25, 25, 113, 117, 117, 117, 25, 25, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 40, 41, 22, 23, 24, 25, 29] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 478 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086669 none COC(=O)C1=CC(NN=CC2=CC=C(OC(C)C(=O)[O-])C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 95, 25, 95, 25, 25, 8, 4, 4, 1, 1, 1, 1, 1, 1, 9, 24, 24, 33, 33, 1, 1, 25, 25, 25, 25, 95, 95, 95, 25, 8, 4, 1, 1, 24, 24, 24, 24, 1, 1, 25, 25, 25, 25, 25] 201 rigid atoms, others: [32, 33, 38, 39, 9, 10, 11, 12, 13, 14, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 331 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086669 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086669 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086669/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086669 Building REAL300000086670 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086670' /scratch/stefan/7769667/working/building/REAL300000086670 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086670 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086670/0 /scratch/stefan/7769667/working/building/REAL300000086670 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/700 `/scratch/stefan/7769667/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)=CC=C1C) `REAL300000086670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086670 none COC(=O)C1=CC(NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 18, 18, 53, 53, 53, 120, 138, 138, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 12, 12, 12, 1, 6, 18, 53, 120, 120, 53, 53, 53, 53, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 40, 41, 23, 24, 25, 26, 30] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 463 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086670 none COC(=O)C1=CC(NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 53, 167, 53, 53, 15, 7, 7, 1, 1, 1, 1, 1, 8, 12, 12, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 167, 167, 167, 53, 15, 7, 1, 8, 8, 1, 1, 1, 1, 53, 53, 53, 53, 53] 201 rigid atoms, others: [33, 36, 37, 38, 39, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 441 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086670 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086670 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086670/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086670 Building REAL300000086671 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086671' /scratch/stefan/7769667/working/building/REAL300000086671 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086671 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086671/0 /scratch/stefan/7769667/working/building/REAL300000086671 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/701 `/scratch/stefan/7769667/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=C(C)N2)=CC=C1C) `REAL300000086671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086671 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=C(C)N2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 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: [13, 13, 1, 13, 1, 1, 1, 1, 12, 69, 69, 87, 87, 87, 99, 99, 87, 87, 87, 1, 1, 1, 1, 13, 13, 13, 1, 12, 69, 87, 87, 87, 87, 87, 1, 1, 2, 2, 2] 178 rigid atoms, others: [2, 35, 4, 5, 6, 7, 34, 19, 20, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086671 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=C(C)N2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 87, 178, 87, 87, 24, 5, 5, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 87, 87, 87, 87, 178, 178, 178, 87, 24, 5, 1, 2, 2, 2, 1, 87, 87, 87, 87, 87] 178 rigid atoms, others: [33, 9, 10, 11, 12, 13, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 432 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086671 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086671 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086671/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086671 Building REAL300000086672 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086672' /scratch/stefan/7769667/working/building/REAL300000086672 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086672 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086672/0 /scratch/stefan/7769667/working/building/REAL300000086672 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/702 `/scratch/stefan/7769667/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=CC(C(=O)[O-])=C2)=CC=C1C) `REAL300000086672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086672 none COC(=O)C1=CC(NN=CC2=CC=CC(C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', '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.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 13, 61, 61, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1, 1, 13, 13, 13, 1, 13, 61, 105, 105, 105, 105, 1, 1, 2, 2, 2] 199 rigid atoms, others: [33, 2, 4, 5, 6, 7, 34, 19, 20, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086672 none COC(=O)C1=CC(NN=CC2=CC=CC(C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', '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.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 105, 199, 105, 105, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 105, 105, 104, 104, 199, 199, 199, 105, 32, 8, 1, 1, 1, 1, 105, 105, 105, 105, 105] 199 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 479 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086672 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086672 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086672/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086672 Building REAL300000086673 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086673' /scratch/stefan/7769667/working/building/REAL300000086673 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086673 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086673/0 /scratch/stefan/7769667/working/building/REAL300000086673 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/703 `/scratch/stefan/7769667/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=C(C)C2=CC=CC(OCCCC(=O)[O-])=C2)=CC=C1C) `REAL300000086673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086673 none COC(=O)C1=CC(NN=C(C)C2=CC=CC(OCCCC(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 1, 1, 1, 1, 2, 4, 4, 4, 11, 11, 11, 11, 11, 29, 67, 89, 116, 166, 166, 11, 1, 1, 1, 1, 7, 7, 7, 1, 2, 5, 5, 5, 11, 11, 11, 67, 67, 89, 89, 116, 116, 11, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 46, 47, 24, 25, 26, 27, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50]) total number of confs: 699 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086673 none COC(=O)C1=CC(NN=C(C)C2=CC=CC(OCCCC(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 38, 11, 11, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 20, 39, 48, 68, 68, 1, 11, 11, 11, 11, 38, 38, 38, 11, 7, 5, 5, 5, 1, 1, 1, 20, 20, 38, 38, 48, 48, 1, 11, 11, 11, 11, 11] 201 rigid atoms, others: [45, 36, 37, 38, 9, 11, 12, 13, 14, 15, 16, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50]) total number of confs: 371 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086673 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086673 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086673/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086673 Building REAL300000086674 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086674' /scratch/stefan/7769667/working/building/REAL300000086674 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086674 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086674/0 /scratch/stefan/7769667/working/building/REAL300000086674 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/704 `/scratch/stefan/7769667/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)=CC=C1C) `REAL300000086674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086674 none COC(=O)C1=CC(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 16, 16, 24, 24, 24, 24, 24, 24, 82, 129, 129, 155, 155, 24, 24, 1, 1, 1, 1, 11, 11, 11, 1, 16, 16, 16, 16, 24, 24, 24, 24, 24, 24, 129, 129, 129, 129, 24, 24, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 2, 4, 5, 6, 7, 49, 50, 25, 26, 27, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53]) total number of confs: 548 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086674 none COC(=O)C1=CC(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 24, 83, 24, 24, 10, 10, 4, 2, 4, 2, 1, 1, 1, 1, 1, 1, 9, 19, 19, 24, 24, 1, 1, 24, 24, 24, 24, 83, 83, 83, 24, 4, 4, 4, 4, 2, 2, 2, 2, 1, 1, 19, 19, 19, 19, 1, 1, 24, 24, 24, 24, 24] 201 rigid atoms, others: [48, 41, 42, 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, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 49, 50, 51, 52, 53]) total number of confs: 276 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086674 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086674 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086674/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086674 Building REAL300000086675 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086675' /scratch/stefan/7769667/working/building/REAL300000086675 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086675 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086675/0 /scratch/stefan/7769667/working/building/REAL300000086675 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/705 `/scratch/stefan/7769667/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)=CC=C1C) `REAL300000086675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086675 none COC(=O)C1=CC(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', '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.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, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 10, 1, 1, 1, 1, 6, 6, 18, 18, 26, 26, 26, 26, 26, 26, 85, 115, 151, 151, 26, 26, 1, 1, 1, 1, 10, 10, 10, 1, 18, 18, 18, 18, 26, 26, 26, 26, 26, 26, 115, 115, 26, 26, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 46, 47, 24, 25, 26, 27, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50]) total number of confs: 522 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086675 none COC(=O)C1=CC(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', '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.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, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 26, 88, 26, 26, 10, 10, 4, 2, 4, 2, 1, 1, 1, 1, 1, 1, 6, 13, 25, 25, 1, 1, 26, 26, 26, 26, 88, 88, 88, 26, 4, 4, 4, 4, 2, 2, 2, 2, 1, 1, 13, 13, 1, 1, 26, 26, 26, 26, 26] 201 rigid atoms, others: [45, 40, 41, 12, 13, 14, 15, 16, 17, 22, 23, 44] 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, 33, 34, 35, 36, 37, 38, 39, 42, 43, 46, 47, 48, 49, 50]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086675 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086675 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086675/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086675 Building REAL300000086676 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086676' /scratch/stefan/7769667/working/building/REAL300000086676 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086676 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086676/0 /scratch/stefan/7769667/working/building/REAL300000086676 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/706 `/scratch/stefan/7769667/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=C(C)C2=CC=CC(OC(C)C(=O)[O-])=C2)=CC=C1C) `REAL300000086676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086676 none COC(=O)C1=CC(NN=C(C)C2=CC=CC(OC(C)C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 12, 12, 12, 29, 29, 29, 29, 29, 80, 137, 137, 150, 150, 29, 1, 1, 1, 1, 9, 9, 9, 1, 6, 13, 13, 13, 29, 29, 29, 137, 137, 137, 137, 29, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 43, 44, 23, 24, 25, 26, 30] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 501 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086676 none COC(=O)C1=CC(NN=C(C)C2=CC=CC(OC(C)C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 110, 29, 29, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 19, 19, 23, 23, 1, 29, 29, 29, 29, 110, 110, 110, 29, 10, 5, 5, 5, 1, 1, 1, 19, 19, 19, 19, 1, 29, 29, 29, 29, 29] 201 rigid atoms, others: [35, 36, 37, 9, 42, 11, 12, 13, 14, 15, 16, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 338 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086676 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086676 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086676/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086676 Building REAL300000086677 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086677' /scratch/stefan/7769667/working/building/REAL300000086677 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086677 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086677/0 /scratch/stefan/7769667/working/building/REAL300000086677 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/707 `/scratch/stefan/7769667/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)=CC=C1C) `REAL300000086677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086677 none COC(=O)C1=CC(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 10, 1, 1, 1, 1, 4, 4, 15, 15, 25, 25, 25, 25, 25, 25, 96, 98, 98, 149, 149, 25, 25, 1, 1, 1, 1, 10, 10, 10, 1, 15, 15, 15, 15, 25, 25, 25, 25, 25, 25, 98, 98, 98, 98, 25, 25, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 2, 4, 5, 6, 7, 49, 50, 25, 26, 27, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086677 none COC(=O)C1=CC(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 25, 84, 25, 25, 10, 10, 3, 2, 3, 2, 1, 1, 1, 1, 1, 1, 6, 8, 9, 18, 18, 1, 1, 25, 25, 25, 25, 84, 84, 84, 25, 3, 3, 3, 3, 2, 2, 2, 2, 1, 1, 8, 8, 8, 8, 1, 1, 25, 25, 25, 25, 25] 201 rigid atoms, others: [48, 41, 42, 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, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 49, 50, 51, 52, 53]) total number of confs: 246 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086677 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086677 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086677/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086677 Building REAL300000086678 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086678' /scratch/stefan/7769667/working/building/REAL300000086678 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086678 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086678/0 /scratch/stefan/7769667/working/building/REAL300000086678 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/708 `/scratch/stefan/7769667/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=C(C)C2=CSC(C(=O)[O-])=C2)=CC=C1C) `REAL300000086678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086678 none COC(=O)C1=CC(NN=C(C)C2=CSC(C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 5, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 42, 42, 42, 111, 111, 111, 111, 111, 111, 111, 1, 1, 1, 1, 13, 13, 13, 1, 10, 43, 43, 43, 111, 111, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 2, 4, 5, 6, 7, 34, 19, 20, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086678 none COC(=O)C1=CC(NN=C(C)C2=CSC(C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 5, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 111, 201, 111, 111, 34, 12, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 111, 111, 111, 111, 201, 201, 201, 111, 34, 12, 12, 12, 1, 1, 111, 111, 111, 111, 111] 201 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 489 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086678 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086678 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086678/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086678 Building REAL300000086679 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086679' /scratch/stefan/7769667/working/building/REAL300000086679 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086679 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086679/0 /scratch/stefan/7769667/working/building/REAL300000086679 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/709 `/scratch/stefan/7769667/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)=CC=C1C) `REAL300000086679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086679 none COC(=O)C1=CC(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 49, 49, 49, 80, 80, 49, 103, 103, 75, 103, 103, 49, 1, 1, 1, 1, 13, 13, 13, 1, 49, 49, 49, 103, 103, 75, 103, 103, 49, 49, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 40, 41, 22, 23, 24, 25, 29] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 425 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: REAL300000086679 none COC(=O)C1=CC(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 103, 201, 103, 103, 40, 40, 5, 5, 5, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 103, 103, 103, 103, 201, 201, 201, 103, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 103, 103, 103, 103, 103] 201 rigid atoms, others: [33, 34, 35, 36, 37, 11, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 441 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086679 none COC(=O)C1=CC(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 177, 49, 49, 13, 13, 1, 1, 1, 1, 1, 3, 3, 1, 5, 5, 2, 5, 5, 1, 49, 49, 49, 49, 177, 177, 177, 49, 1, 1, 1, 5, 5, 2, 5, 5, 1, 1, 49, 49, 49, 49, 49] 201 rigid atoms, others: [32, 38, 39, 8, 9, 10, 11, 12, 15, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 399 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086679 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086679 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086679/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086679 Building REAL300000086680 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086680' /scratch/stefan/7769667/working/building/REAL300000086680 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086680 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086680/0 /scratch/stefan/7769667/working/building/REAL300000086680 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/710 `/scratch/stefan/7769667/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(N=NC(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)=CC=C1C) `REAL300000086680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086680 none COC(=O)C1=CC(N=NC(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 41, 41, 58, 58, 58, 58, 58, 94, 122, 122, 58, 58, 58, 1, 1, 1, 1, 11, 11, 11, 1, 41, 41, 41, 41, 58, 58, 94, 94, 58, 58, 58, 58, 58, 58, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 45, 46, 23, 24, 25, 26, 30] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 509 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086680 none COC(=O)C1=CC(N=NC(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 58, 171, 58, 58, 21, 21, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 11, 11, 1, 1, 1, 58, 58, 58, 58, 171, 171, 171, 58, 4, 4, 4, 4, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2, 58, 58, 58, 58, 58] 201 rigid atoms, others: [35, 36, 9, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 438 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086680 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086680 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086680/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086680 Building REAL300000086681 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086681' /scratch/stefan/7769667/working/building/REAL300000086681 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086681 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086681/0 /scratch/stefan/7769667/working/building/REAL300000086681 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/711 `/scratch/stefan/7769667/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(N=NC(C)CCCCCCC(=O)[O-])=CC=C1C) `REAL300000086681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086681 none COC(=O)C1=CC(N=NC(C)CCCCCCC(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 26, 26, 46, 46, 46, 46, 46, 98, 106, 106, 1, 1, 1, 1, 9, 9, 9, 1, 26, 26, 26, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 98, 98, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 44, 45, 20, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 477 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086681 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086681 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086681/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086681 Building REAL300000086682 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086682' /scratch/stefan/7769667/working/building/REAL300000086682 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086682 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086682/0 /scratch/stefan/7769667/working/building/REAL300000086682 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/712 `/scratch/stefan/7769667/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(N=NC2CCC(CC(=O)[O-])C2C)=CC=C1C) `REAL300000086682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086682 none COC(=O)C1=CC(N=NC2CCC(CC(=O)[O-])C2C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 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, 8, 8, 53, 53, 53, 53, 77, 83, 83, 53, 53, 1, 1, 1, 1, 13, 13, 13, 1, 53, 53, 53, 53, 53, 53, 77, 77, 53, 53, 53, 53, 1, 1, 2, 2, 2] 120 rigid atoms, others: [2, 4, 5, 6, 7, 40, 39, 19, 20, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 315 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086682 none COC(=O)C1=CC(N=NC2CCC(CC(=O)[O-])C2C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 53, 120, 53, 53, 11, 11, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 53, 53, 53, 53, 120, 120, 120, 53, 1, 1, 1, 1, 1, 1, 3, 3, 1, 2, 2, 2, 53, 53, 53, 53, 53] 120 rigid atoms, others: [32, 35, 8, 9, 10, 11, 12, 13, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 301 number of broken/clashed sets: 119 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086682 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086682 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086682/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086682 Building REAL300000086683 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086683' /scratch/stefan/7769667/working/building/REAL300000086683 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086683 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086683/0 /scratch/stefan/7769667/working/building/REAL300000086683 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/713 `/scratch/stefan/7769667/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CNC(C(=O)[O-])=C2)=CC=C1C) `REAL300000086683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086683 none COC(=O)C1=CC(NN=CC2=CNC(C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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: [13, 13, 1, 13, 1, 1, 1, 1, 12, 59, 59, 108, 108, 108, 108, 108, 108, 108, 1, 1, 1, 1, 13, 13, 13, 1, 12, 59, 108, 108, 108, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 2, 4, 5, 6, 7, 18, 19, 20, 21, 25, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086683 none COC(=O)C1=CC(NN=CC2=CNC(C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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: [201, 201, 108, 201, 108, 108, 33, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 201, 201, 201, 108, 33, 7, 1, 1, 1, 108, 108, 109, 109, 109] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 471 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086683 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086683 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086683/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086683 Building REAL300000086684 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086684' /scratch/stefan/7769667/working/building/REAL300000086684 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086684 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086684/0 /scratch/stefan/7769667/working/building/REAL300000086684 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/714 `/scratch/stefan/7769667/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(N=NC(C)CC2(C(=O)[O-])CCC2)=CC=C1C) `REAL300000086684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086684 none COC(=O)C1=CC(N=NC(C)CC2(C(=O)[O-])CCC2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 39, 39, 72, 100, 111, 111, 100, 100, 100, 1, 1, 1, 1, 12, 12, 12, 1, 39, 39, 39, 39, 72, 72, 100, 100, 100, 100, 100, 100, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 40, 39, 19, 20, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 455 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086684 none COC(=O)C1=CC(N=NC(C)CC2(C(=O)[O-])CCC2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 100, 201, 100, 100, 43, 43, 8, 5, 8, 1, 1, 1, 3, 3, 1, 1, 1, 100, 100, 100, 100, 201, 201, 201, 100, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 11, 12, 13, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43]) total number of confs: 473 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086684 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086684 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086684/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086684 Building REAL300000086685 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086685' /scratch/stefan/7769667/working/building/REAL300000086685 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL300000086685 as failed and skipping /scratch/stefan/7769667/working /scratch/stefan/7769667 `/scratch/stefan/7769667/working/building/REAL300000086685' -> `/scratch/stefan/7769667/failed/REAL300000086685' Building REAL300000086686 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086686' /scratch/stefan/7769667/working/building/REAL300000086686 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086686 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086686/0 /scratch/stefan/7769667/working/building/REAL300000086686 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/715 `/scratch/stefan/7769667/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=C(C)C=C2C)=CC=C1C) `REAL300000086686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086686 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=C(C)C=C2C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 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: [13, 13, 1, 13, 1, 1, 1, 1, 4, 16, 16, 39, 39, 39, 54, 54, 39, 39, 39, 39, 39, 1, 1, 1, 1, 13, 13, 13, 1, 4, 16, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 2, 2, 2] 101 rigid atoms, others: [2, 4, 5, 6, 7, 40, 39, 21, 22, 23, 24, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086686 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=C(C)C=C2C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 39, 101, 39, 39, 28, 10, 10, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 39, 39, 39, 39, 101, 101, 101, 39, 28, 10, 1, 2, 2, 2, 1, 2, 2, 2, 39, 39, 39, 39, 39] 101 rigid atoms, others: [35, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086686 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086686 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086686/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086686 Building REAL300000086687 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086687' /scratch/stefan/7769667/working/building/REAL300000086687 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086687 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086687/0 /scratch/stefan/7769667/working/building/REAL300000086687 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/716 `/scratch/stefan/7769667/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=CC(C(=O)[O-])=C2Cl)=CC=C1C) `REAL300000086687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086687 none COC(=O)C1=CC(NN=CC2=CC=CC(C(=O)[O-])=C2Cl)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 52, 53, 101, 101, 101, 101, 101, 104, 104, 101, 101, 1, 1, 1, 1, 13, 13, 13, 1, 10, 52, 101, 101, 101, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 2, 4, 5, 6, 7, 34, 20, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086687 none COC(=O)C1=CC(NN=CC2=CC=CC(C(=O)[O-])=C2Cl)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 101, 201, 101, 101, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 101, 101, 101, 101, 201, 201, 201, 101, 30, 6, 1, 1, 1, 101, 101, 101, 101, 101] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 481 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086687 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086687 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086687/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086687 Building REAL300000086688 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086688' /scratch/stefan/7769667/working/building/REAL300000086688 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086688 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086688/0 /scratch/stefan/7769667/working/building/REAL300000086688 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/717 `/scratch/stefan/7769667/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)=CC=C1C) `REAL300000086688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086688 none COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 8, 31, 31, 94, 94, 94, 94, 116, 116, 94, 94, 94, 1, 1, 1, 1, 13, 13, 13, 1, 8, 31, 94, 95, 94, 1, 1, 2, 2, 2] 173 rigid atoms, others: [33, 2, 4, 5, 6, 7, 34, 20, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086688 none COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 95, 173, 95, 94, 42, 10, 10, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 95, 95, 95, 95, 173, 173, 173, 94, 42, 10, 1, 1, 1, 95, 95, 95, 95, 95] 173 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 434 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086688 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086688 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086688/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086688 Building REAL300000086689 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086689' /scratch/stefan/7769667/working/building/REAL300000086689 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086689 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086689/0 /scratch/stefan/7769667/working/building/REAL300000086689 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/718 `/scratch/stefan/7769667/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(C=CC(=O)[O-])O2)=CC=C1C) `REAL300000086689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086689 none COC(=O)C1=CC(NN=CC2=CC=C(C=CC(=O)[O-])O2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 28, 28, 44, 44, 44, 44, 109, 109, 139, 139, 44, 1, 1, 1, 1, 11, 11, 11, 1, 6, 28, 44, 44, 109, 109, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 35, 4, 5, 6, 7, 34, 20, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 392 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086689 none COC(=O)C1=CC(NN=CC2=CC=C(C=CC(=O)[O-])O2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 156, 44, 44, 13, 5, 5, 1, 1, 1, 1, 1, 1, 12, 12, 29, 29, 1, 44, 44, 44, 44, 156, 156, 156, 44, 13, 5, 1, 1, 12, 12, 44, 44, 44, 44, 44] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 451 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086689 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086689 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086689/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086689 Building REAL300000086690 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086690' /scratch/stefan/7769667/working/building/REAL300000086690 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086690 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086690/0 /scratch/stefan/7769667/working/building/REAL300000086690 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/719 `/scratch/stefan/7769667/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)=CC=C1C) `REAL300000086690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086690 none COC(=O)C1=CC(NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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, 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, 1, 9, 1, 1, 1, 1, 4, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 9, 9, 9, 1, 4, 6, 8, 8, 8, 8, 8, 1, 1, 2, 2, 2] 15 rigid atoms, others: [2, 4, 5, 6, 7, 22, 23, 24, 25, 38, 29, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086690 none COC(=O)C1=CC(NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 8, 15, 8, 8, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 8, 8, 8, 8, 15, 15, 15, 8, 6, 4, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 15 rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086690 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086690 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086690/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086690 Building REAL300000086691 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086691' /scratch/stefan/7769667/working/building/REAL300000086691 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086691 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086691/0 /scratch/stefan/7769667/working/building/REAL300000086691 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/720 `/scratch/stefan/7769667/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])N=C2)=CC=C1C) `REAL300000086691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086691 none COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])N=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 8, 28, 28, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 10, 10, 10, 1, 8, 28, 57, 57, 57, 1, 1, 2, 2, 2] 94 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 19, 20, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086691 none COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])N=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 57, 94, 57, 57, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 94, 94, 94, 57, 30, 9, 1, 1, 1, 57, 57, 57, 57, 57] 94 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086691 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086691 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086691/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086691 Building REAL300000086692 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086692' /scratch/stefan/7769667/working/building/REAL300000086692 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086692 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086692/0 /scratch/stefan/7769667/working/building/REAL300000086692 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/721 `/scratch/stefan/7769667/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)=CC=C1C) `REAL300000086692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086692 none COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 326 conformations in input total number of sets (complete confs): 326 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 8, 33, 33, 87, 87, 87, 87, 102, 102, 87, 88, 87, 1, 1, 1, 1, 13, 13, 13, 1, 8, 33, 87, 87, 176, 87, 1, 1, 2, 2, 2] 326 rigid atoms, others: [2, 35, 4, 5, 6, 7, 34, 20, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 402 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086692 none COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 326 conformations in input total number of sets (complete confs): 326 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 88, 163, 88, 87, 39, 8, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 88, 88, 88, 88, 163, 163, 163, 87, 39, 8, 1, 1, 2, 1, 88, 88, 88, 88, 88] 326 rigid atoms, others: [33, 9, 10, 11, 12, 13, 14, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 34, 35, 36, 37, 38]) total number of confs: 424 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086692 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086692 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086692/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086692 Building REAL300000086693 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086693' /scratch/stefan/7769667/working/building/REAL300000086693 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086693 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086693/0 /scratch/stefan/7769667/working/building/REAL300000086693 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/722 `/scratch/stefan/7769667/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(C)C(C(=O)[O-])=C2)=CC=C1C) `REAL300000086693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086693 none COC(=O)C1=CC(NN=CC2=CC=C(C)C(C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 4, 17, 17, 37, 37, 37, 37, 37, 37, 38, 38, 37, 1, 1, 1, 1, 13, 13, 13, 1, 4, 17, 37, 37, 38, 38, 38, 37, 1, 1, 2, 2, 2] 68 rigid atoms, others: [2, 4, 5, 6, 7, 20, 21, 22, 23, 36, 27, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086693 none COC(=O)C1=CC(NN=CC2=CC=C(C)C(C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 37, 68, 37, 37, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 37, 37, 37, 68, 68, 68, 37, 26, 8, 1, 1, 2, 2, 2, 1, 37, 37, 38, 38, 38] 68 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086693 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086693 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086693/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086693 Building REAL300000086694 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086694' /scratch/stefan/7769667/working/building/REAL300000086694 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086694 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086694/0 /scratch/stefan/7769667/working/building/REAL300000086694 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/723 `/scratch/stefan/7769667/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=C(Cl)S2)=CC=C1C) `REAL300000086694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086694 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=C(Cl)S2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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] 0 hydrogens 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, 1, 8, 31, 32, 76, 76, 76, 122, 122, 75, 76, 76, 1, 1, 1, 1, 12, 12, 12, 1, 8, 31, 76, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 19, 20, 21, 22, 26, 30, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 32, 33, 34]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086694 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=C(Cl)S2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 76, 201, 76, 76, 24, 7, 7, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 76, 76, 76, 76, 201, 201, 201, 76, 24, 7, 1, 76, 76, 76, 76, 76] 201 rigid atoms, others: [9, 10, 11, 12, 13, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 498 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086694 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086694 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086694/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086694 Building REAL300000086695 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086695' /scratch/stefan/7769667/working/building/REAL300000086695 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086695 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086695/0 /scratch/stefan/7769667/working/building/REAL300000086695 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/724 `/scratch/stefan/7769667/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=NN2C)=CC=C1C) `REAL300000086695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086695 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=NN2C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 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: [13, 13, 1, 13, 1, 1, 1, 1, 12, 62, 63, 94, 94, 94, 94, 94, 94, 94, 93, 1, 1, 1, 1, 13, 13, 13, 1, 12, 62, 94, 94, 94, 94, 1, 1, 2, 2, 2] 191 rigid atoms, others: [33, 2, 4, 5, 6, 7, 34, 19, 20, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086695 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=NN2C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 94, 191, 93, 93, 35, 8, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 93, 93, 93, 93, 191, 191, 191, 93, 35, 8, 1, 2, 2, 2, 94, 94, 94, 94, 94] 191 rigid atoms, others: [9, 10, 11, 12, 13, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 483 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086695 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086695 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086695/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086695 Building REAL300000086696 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086696' /scratch/stefan/7769667/working/building/REAL300000086696 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086696 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086696/0 /scratch/stefan/7769667/working/building/REAL300000086696 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/725 `/scratch/stefan/7769667/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=CC=C1C) `REAL300000086696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086696 none COC(=O)C1=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 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: [12, 12, 1, 12, 1, 1, 1, 1, 6, 20, 20, 38, 38, 38, 38, 152, 152, 152, 152, 152, 152, 152, 152, 152, 38, 1, 1, 1, 1, 12, 12, 12, 1, 6, 20, 38, 38, 152, 152, 304, 152, 1, 1, 2, 2, 2] 402 rigid atoms, others: [32, 2, 4, 5, 6, 7, 41, 42, 25, 26, 27, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 541 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086696 none COC(=O)C1=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 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: [201, 201, 152, 201, 152, 152, 66, 32, 32, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 152, 152, 152, 152, 201, 201, 201, 152, 66, 32, 12, 12, 1, 1, 2, 1, 152, 152, 152, 152, 152] 402 rigid atoms, others: [37, 38, 40, 13, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 41, 42, 43, 44, 45]) total number of confs: 510 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086696 none COC(=O)C1=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 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: [132, 132, 38, 132, 38, 38, 13, 5, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 13, 13, 12, 1, 38, 38, 38, 38, 132, 132, 132, 38, 13, 5, 1, 1, 12, 12, 24, 12, 38, 38, 38, 38, 38] 402 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 364 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086696 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086696 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086696/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086696 Building REAL300000086697 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086697' /scratch/stefan/7769667/working/building/REAL300000086697 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086697 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086697/0 /scratch/stefan/7769667/working/building/REAL300000086697 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/726 `/scratch/stefan/7769667/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=CN2C)=CC=C1C) `REAL300000086697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086697 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=CN2C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.3', 'C.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 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: [12, 12, 1, 12, 1, 1, 1, 1, 12, 66, 66, 97, 97, 97, 97, 97, 97, 97, 97, 1, 1, 1, 1, 12, 12, 12, 1, 12, 66, 97, 97, 97, 97, 97, 1, 1, 2, 2, 2] 193 rigid atoms, others: [2, 35, 4, 5, 6, 7, 34, 19, 20, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086697 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=CN2C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.3', 'C.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 97, 193, 97, 97, 37, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 193, 193, 193, 97, 37, 9, 1, 1, 2, 2, 2, 97, 97, 97, 97, 97] 193 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 473 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086697 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086697 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086697/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086697 Building REAL300000086698 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086698' /scratch/stefan/7769667/working/building/REAL300000086698 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086698 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086698/0 /scratch/stefan/7769667/working/building/REAL300000086698 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/727 `/scratch/stefan/7769667/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=CC=C2N(C)C)=CC=C1C) `REAL300000086698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086698 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=CC=C2N(C)C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 10, 49, 49, 108, 108, 108, 108, 108, 108, 108, 108, 108, 109, 109, 1, 1, 1, 1, 12, 12, 12, 1, 10, 49, 108, 108, 108, 109, 109, 109, 109, 109, 109, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 41, 42, 22, 23, 24, 25, 29] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 188 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086698 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=CC=C2N(C)C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 108, 201, 108, 108, 36, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 108, 108, 108, 108, 201, 201, 201, 108, 36, 12, 1, 1, 1, 4, 4, 4, 3, 3, 3, 108, 108, 108, 108, 108] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 502 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086698 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086698 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086698/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086698 Building REAL300000086699 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086699' /scratch/stefan/7769667/working/building/REAL300000086699 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086699 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086699/0 /scratch/stefan/7769667/working/building/REAL300000086699 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/728 `/scratch/stefan/7769667/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=CC=C1C) `REAL300000086699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086699 none COC(=O)C1=CC(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 1, 7, 21, 21, 43, 43, 43, 43, 153, 153, 153, 153, 153, 153, 153, 153, 43, 1, 1, 1, 1, 12, 12, 12, 1, 7, 21, 43, 43, 153, 153, 153, 153, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 40, 41, 24, 25, 26, 27, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086699 none COC(=O)C1=CC(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 153, 201, 153, 153, 91, 47, 47, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 153, 153, 153, 153, 201, 201, 201, 153, 91, 47, 12, 12, 1, 1, 1, 1, 153, 153, 153, 153, 153] 201 rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 523 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086699 none COC(=O)C1=CC(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 43, 134, 43, 43, 21, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 12, 1, 43, 43, 43, 43, 134, 134, 134, 43, 20, 6, 1, 1, 12, 12, 12, 12, 43, 43, 43, 43, 43] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 350 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086699 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086699 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086699/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086699 Building REAL300000086700 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086700' /scratch/stefan/7769667/working/building/REAL300000086700 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086700 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086700/0 /scratch/stefan/7769667/working/building/REAL300000086700 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/729 `/scratch/stefan/7769667/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=CC=C2OC)=CC=C1C) `REAL300000086700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086700 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=CC=C2OC)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [13, 13, 1, 13, 1, 1, 1, 1, 6, 30, 31, 85, 85, 85, 85, 85, 85, 85, 85, 85, 110, 1, 1, 1, 1, 13, 13, 13, 1, 6, 30, 84, 85, 85, 110, 110, 110, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 24, 38, 28, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086700 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=CC=C2OC)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [201, 201, 85, 201, 84, 84, 32, 12, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 3, 84, 84, 84, 84, 201, 201, 201, 85, 32, 12, 1, 1, 1, 4, 4, 4, 84, 84, 85, 85, 85] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 527 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086700 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086700 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086700/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086700 Building REAL300000086701 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086701' /scratch/stefan/7769667/working/building/REAL300000086701 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086701 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086701/0 /scratch/stefan/7769667/working/building/REAL300000086701 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/730 `/scratch/stefan/7769667/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=CC=C1C) `REAL300000086701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086701 none COC(=O)C1=CC(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 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: [9, 9, 1, 9, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 9, 9, 9, 1, 4, 4, 7, 7, 7, 7, 1, 1, 2, 2, 2] 13 rigid atoms, others: [2, 4, 5, 6, 7, 25, 22, 23, 24, 36, 29, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086701 none COC(=O)C1=CC(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 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, 7, 13, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 3, 3, 1, 1, 1, 1, 7, 7, 7, 7, 7] 13 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086701 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086701 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086701/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086701 Building REAL300000086702 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086702' /scratch/stefan/7769667/working/building/REAL300000086702 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086702 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086702/0 /scratch/stefan/7769667/working/building/REAL300000086702 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/731 `/scratch/stefan/7769667/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=CO2)=CC=C1C) `REAL300000086702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086702 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=CO2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 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] 0 hydrogens 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, 12, 49, 50, 103, 103, 103, 103, 103, 103, 103, 1, 1, 1, 1, 13, 13, 13, 1, 12, 49, 103, 103, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 18, 19, 20, 21, 25, 30, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086702 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=CO2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 103, 201, 103, 103, 39, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 201, 201, 201, 103, 39, 7, 1, 1, 103, 103, 103, 103, 103] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 487 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086702 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086702 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086702/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086702 Building REAL300000086703 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086703' /scratch/stefan/7769667/working/building/REAL300000086703 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086703 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086703/0 /scratch/stefan/7769667/working/building/REAL300000086703 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/732 `/scratch/stefan/7769667/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=CC=C2Br)=CC=C1C) `REAL300000086703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086703 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=CC=C2Br)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7] 0 hydrogens 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, 10, 36, 36, 110, 110, 110, 110, 110, 110, 110, 110, 110, 1, 1, 1, 1, 13, 13, 13, 1, 10, 36, 110, 110, 110, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 2, 4, 5, 6, 7, 34, 20, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086703 none COC(=O)C1=CC(NN=CC2=CC(C(=O)[O-])=CC=C2Br)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 110, 201, 110, 110, 48, 12, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 110, 110, 110, 110, 201, 201, 201, 110, 48, 12, 1, 1, 1, 110, 110, 110, 110, 110] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 481 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086703 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086703 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086703/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086703 Building REAL300000086704 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086704' /scratch/stefan/7769667/working/building/REAL300000086704 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086704 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086704/0 /scratch/stefan/7769667/working/building/REAL300000086704 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/733 `/scratch/stefan/7769667/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C(OC)=C2)=CC=C1C) `REAL300000086704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086704 none COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C(OC)=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 6, 22, 22, 64, 64, 64, 64, 91, 91, 64, 65, 107, 64, 1, 1, 1, 1, 11, 11, 11, 1, 6, 22, 64, 64, 107, 107, 107, 64, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 24, 38, 28, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086704 none COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C(OC)=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 65, 189, 65, 64, 20, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 1, 65, 65, 65, 65, 189, 189, 189, 64, 20, 6, 1, 1, 3, 3, 3, 1, 65, 65, 65, 65, 65] 201 rigid atoms, others: [32, 36, 9, 10, 11, 12, 13, 14, 17, 18, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 456 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086704 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086704 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086704/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086704 Building REAL300000086705 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086705' /scratch/stefan/7769667/working/building/REAL300000086705 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086705 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086705/0 /scratch/stefan/7769667/working/building/REAL300000086705 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/734 `/scratch/stefan/7769667/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)=CC=C1C) `REAL300000086705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086705 none COC(=O)C1=CC(NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 55, 55, 115, 115, 115, 55, 62, 115, 115, 115, 115, 115, 1, 1, 1, 1, 13, 13, 13, 1, 12, 55, 115, 115, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 2, 4, 5, 6, 7, 34, 21, 22, 23, 24, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 514 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086705 none COC(=O)C1=CC(NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 48, 70, 48, 48, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 48, 48, 48, 48, 70, 70, 70, 48, 29, 7, 1, 1, 48, 48, 48, 48, 48] 70 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 185 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086705 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086705 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086705/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086705 Building REAL300000086706 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086706' /scratch/stefan/7769667/working/building/REAL300000086706 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086706 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086706/0 /scratch/stefan/7769667/working/building/REAL300000086706 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/735 `/scratch/stefan/7769667/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC(C)=C(C(=O)[O-])N2)=CC=C1C) `REAL300000086706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086706 none COC(=O)C1=CC(NN=CC2=CC(C)=C(C(=O)[O-])N2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 11, 11, 8, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 11, 1, 11, 1, 1, 1, 1, 10, 35, 35, 86, 86, 86, 86, 86, 108, 108, 86, 1, 1, 1, 1, 11, 11, 11, 1, 10, 35, 86, 86, 86, 86, 86, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 35, 4, 5, 6, 7, 34, 19, 20, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086706 none COC(=O)C1=CC(NN=CC2=CC(C)=C(C(=O)[O-])N2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 11, 11, 8, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [201, 201, 86, 201, 86, 86, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 86, 86, 86, 86, 201, 201, 201, 86, 26, 7, 1, 2, 2, 2, 1, 86, 86, 86, 86, 86] 201 rigid atoms, others: [33, 9, 10, 11, 12, 13, 14, 15, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 501 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086706 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086706 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086706/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086706 Building REAL300000086707 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086707' /scratch/stefan/7769667/working/building/REAL300000086707 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086707 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086707/0 /scratch/stefan/7769667/working/building/REAL300000086707 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/736 `/scratch/stefan/7769667/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)=CC=C1C) `REAL300000086707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086707 none COC(=O)C1=CC(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 292 conformations in input total number of sets (complete confs): 292 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 8, 39, 39, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1, 1, 1, 12, 12, 12, 1, 8, 39, 176, 88, 88, 88, 88, 88, 1, 1, 2, 2, 2] 292 rigid atoms, others: [2, 4, 5, 6, 7, 40, 41, 24, 25, 26, 27, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 332 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086707 none COC(=O)C1=CC(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 292 conformations in input total number of sets (complete confs): 292 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 88, 146, 88, 88, 38, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 146, 146, 146, 88, 38, 11, 2, 1, 1, 1, 1, 1, 88, 88, 88, 88, 88] 292 rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44]) total number of confs: 378 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086707 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086707 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086707/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086707 Building REAL300000086708 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086708' /scratch/stefan/7769667/working/building/REAL300000086708 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086708 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086708/0 /scratch/stefan/7769667/working/building/REAL300000086708 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/737 `/scratch/stefan/7769667/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CSC(C(=O)[O-])=C2)=CC=C1C) `REAL300000086708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086708 none COC(=O)C1=CC(NN=CC2=CSC(C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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 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, 12, 65, 65, 106, 106, 106, 106, 106, 106, 106, 1, 1, 1, 1, 13, 13, 13, 1, 12, 65, 106, 106, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 18, 19, 20, 21, 25, 30, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086708 none COC(=O)C1=CC(NN=CC2=CSC(C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 106, 201, 106, 106, 41, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 106, 106, 106, 106, 201, 201, 201, 106, 41, 9, 1, 1, 106, 106, 106, 106, 106] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 476 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086708 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086708 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086708/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086708 Building REAL300000086709 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086709' /scratch/stefan/7769667/working/building/REAL300000086709 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086709 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086709/0 /scratch/stefan/7769667/working/building/REAL300000086709 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/738 `/scratch/stefan/7769667/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=C(C)C(C(=O)OC)=C2)=CC=C1OCC(=O)[O-]) `REAL300000086709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086709 none CCOC1=CC(C=NNC2=CC=C(C)C(C(=O)OC)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 11, 12, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 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] 0 hydrogens 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, 7, 1, 1, 1, 1, 1, 4, 4, 8, 12, 12, 12, 12, 12, 12, 41, 41, 41, 12, 1, 1, 1, 1, 7, 30, 45, 45, 9, 9, 9, 9, 9, 1, 4, 8, 12, 12, 13, 13, 13, 41, 41, 41, 12, 1, 1, 30, 30] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 45, 46, 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, 42, 43, 44, 47, 48]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086709 none CCOC1=CC(C=NNC2=CC=C(C)C(C(=O)OC)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 11, 12, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 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] 0 hydrogens 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, 25, 12, 12, 12, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 12, 12, 12, 12, 54, 114, 123, 123, 27, 27, 27, 27, 27, 12, 6, 2, 1, 1, 2, 2, 2, 7, 7, 7, 1, 12, 12, 114, 114] 201 rigid atoms, others: [36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 450 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086709 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086709 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086709/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086709 Building REAL300000086710 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086710' /scratch/stefan/7769667/working/building/REAL300000086710 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086710 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086710/0 /scratch/stefan/7769667/working/building/REAL300000086710 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/739 `/scratch/stefan/7769667/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(CCC(=O)[O-])O2)=CC=C1C) `REAL300000086710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086710 none COC(=O)C1=CC(NN=CC2=CC=C(CCC(=O)[O-])O2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 22, 22, 35, 35, 35, 35, 97, 107, 130, 114, 35, 1, 1, 1, 1, 13, 13, 13, 1, 6, 22, 35, 35, 97, 97, 107, 107, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 20, 21, 22, 23, 36, 27, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 503 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086710 none COC(=O)C1=CC(NN=CC2=CC=C(CCC(=O)[O-])O2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 128, 35, 35, 10, 4, 4, 1, 1, 1, 1, 1, 1, 8, 12, 25, 17, 1, 35, 35, 35, 35, 128, 128, 128, 35, 10, 4, 1, 1, 8, 8, 12, 12, 35, 35, 35, 35, 35] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 385 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086710 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086710 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086710/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086710 Building REAL300000086711 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086711' /scratch/stefan/7769667/working/building/REAL300000086711 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086711 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086711/0 /scratch/stefan/7769667/working/building/REAL300000086711 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/740 `/scratch/stefan/7769667/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)=CC=C1C) `REAL300000086711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086711 none COC(=O)C1=CC(NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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, 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: [13, 13, 1, 13, 1, 1, 1, 1, 8, 35, 36, 97, 97, 97, 97, 97, 100, 100, 97, 97, 97, 97, 1, 1, 1, 1, 13, 13, 13, 1, 8, 35, 97, 97, 97, 97, 97, 1, 1, 2, 2, 2] 161 rigid atoms, others: [2, 4, 5, 6, 7, 22, 23, 24, 25, 38, 29, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086711 none COC(=O)C1=CC(NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 97, 161, 97, 97, 43, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 97, 97, 97, 97, 161, 161, 161, 97, 43, 10, 1, 1, 1, 1, 1, 97, 97, 97, 97, 97] 161 rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41]) total number of confs: 393 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086711 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086711 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086711/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086711 Building REAL300000086712 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086712' /scratch/stefan/7769667/working/building/REAL300000086712 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086712 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086712/0 /scratch/stefan/7769667/working/building/REAL300000086712 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/741 `/scratch/stefan/7769667/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)=CC=C1C) `REAL300000086712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086712 none COC(=O)C1=CC(NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 8, 28, 28, 73, 73, 73, 73, 73, 73, 74, 74, 73, 73, 73, 1, 1, 1, 1, 13, 13, 13, 1, 8, 28, 73, 74, 73, 73, 1, 1, 2, 2, 2] 109 rigid atoms, others: [2, 4, 5, 6, 7, 25, 22, 23, 24, 36, 29, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086712 none COC(=O)C1=CC(NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 74, 109, 74, 73, 36, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 74, 74, 74, 74, 109, 109, 109, 73, 36, 10, 1, 1, 1, 1, 74, 74, 74, 74, 74] 109 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086712 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086712 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086712/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086712 Building REAL300000086713 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086713' /scratch/stefan/7769667/working/building/REAL300000086713 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086713 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086713/0 /scratch/stefan/7769667/working/building/REAL300000086713 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/742 `/scratch/stefan/7769667/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)=CC=C1C) `REAL300000086713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086713 none COC(=O)C1=CC(NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 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, 8, 37, 37, 67, 67, 67, 67, 67, 67, 67, 67, 66, 66, 66, 1, 1, 1, 1, 13, 13, 13, 1, 8, 37, 67, 67, 67, 66, 1, 1, 2, 2, 2] 120 rigid atoms, others: [2, 4, 5, 6, 7, 25, 22, 23, 24, 36, 29, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086713 none COC(=O)C1=CC(NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 66, 120, 66, 66, 26, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 66, 66, 66, 66, 120, 120, 120, 66, 26, 5, 1, 1, 1, 1, 67, 67, 67, 67, 67] 120 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086713 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086713 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086713/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086713 Building REAL300000086714 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086714' /scratch/stefan/7769667/working/building/REAL300000086714 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086714 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086714/0 /scratch/stefan/7769667/working/building/REAL300000086714 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/743 `/scratch/stefan/7769667/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=CC=C1C) `REAL300000086714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086714 none COC(=O)C1=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7] 0 hydrogens 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, 6, 10, 11, 29, 29, 21, 26, 73, 133, 143, 143, 29, 29, 29, 1, 1, 1, 1, 9, 9, 9, 1, 6, 10, 29, 29, 133, 133, 29, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 22, 23, 24, 25, 38, 29, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 494 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086714 none COC(=O)C1=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7] 0 hydrogens 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, 104, 29, 104, 29, 29, 11, 7, 7, 1, 1, 1, 1, 1, 1, 7, 23, 31, 31, 1, 1, 1, 29, 29, 29, 29, 104, 104, 104, 29, 11, 7, 1, 1, 23, 23, 1, 29, 29, 29, 29, 29] 201 rigid atoms, others: [32, 33, 36, 9, 10, 11, 12, 13, 14, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 354 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086714 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086714 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086714/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086714 Building REAL300000086715 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086715' /scratch/stefan/7769667/working/building/REAL300000086715 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086715 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086715/0 /scratch/stefan/7769667/working/building/REAL300000086715 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/744 `/scratch/stefan/7769667/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=CC=C1C) `REAL300000086715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086715 none COC(=O)C1=CC(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 6, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 9, 9, 9, 1, 6, 10, 11, 11, 11, 1, 1, 2, 2, 2] 19 rigid atoms, others: [2, 4, 5, 6, 7, 23, 24, 25, 26, 37, 30, 36] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086715 none COC(=O)C1=CC(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 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, 11, 19, 11, 11, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 19, 19, 19, 11, 7, 5, 1, 1, 1, 11, 11, 11, 11, 11] 19 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086715 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086715 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086715/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086715 Building REAL300000086716 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086716' /scratch/stefan/7769667/working/building/REAL300000086716 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086716 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086716/0 /scratch/stefan/7769667/working/building/REAL300000086716 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/745 `/scratch/stefan/7769667/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C=C2OC)=CC=C1C) `REAL300000086716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086716 none COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C=C2OC)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 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: [13, 13, 1, 13, 1, 1, 1, 1, 8, 35, 35, 74, 74, 74, 74, 74, 74, 74, 74, 74, 89, 1, 1, 1, 1, 13, 13, 13, 1, 8, 35, 74, 74, 74, 89, 89, 89, 1, 1, 2, 2, 2] 132 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 24, 38, 28, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086716 none COC(=O)C1=CC(NN=CC2=CC=C(C(=O)[O-])C=C2OC)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 74, 132, 74, 74, 37, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 74, 74, 74, 74, 132, 132, 132, 74, 37, 10, 1, 1, 1, 4, 4, 4, 74, 74, 74, 74, 74] 132 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086716 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086716 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086716/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086716 Building REAL300000086717 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086717' /scratch/stefan/7769667/working/building/REAL300000086717 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086717 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086717/0 /scratch/stefan/7769667/working/building/REAL300000086717 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/746 `/scratch/stefan/7769667/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=CC=C1C) `REAL300000086717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086717 none COC(=O)C1=CC(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', '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, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 10, 1, 1, 1, 1, 7, 21, 21, 28, 28, 28, 97, 97, 97, 97, 97, 140, 140, 97, 28, 28, 1, 1, 1, 1, 10, 10, 10, 1, 7, 21, 97, 97, 97, 97, 28, 28, 1, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 40, 41, 24, 25, 26, 27, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 424 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086717 none COC(=O)C1=CC(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', '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, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 92, 201, 97, 97, 39, 17, 17, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 97, 97, 97, 97, 201, 201, 201, 97, 39, 17, 1, 1, 1, 1, 12, 12, 97, 97, 97, 97, 97] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 523 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086717 none COC(=O)C1=CC(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', '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, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 28, 106, 28, 28, 10, 4, 4, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 23, 23, 12, 1, 1, 28, 28, 28, 28, 106, 106, 106, 28, 10, 4, 12, 12, 12, 12, 1, 1, 28, 28, 28, 28, 28] 201 rigid atoms, others: [38, 39, 9, 10, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 323 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086717 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086717 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086717/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086717 Building REAL300000086718 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086718' /scratch/stefan/7769667/working/building/REAL300000086718 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086718 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086718/0 /scratch/stefan/7769667/working/building/REAL300000086718 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/747 `/scratch/stefan/7769667/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C=C2)C=N1) `REAL300000086718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086718 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 10, 27, 27, 34, 34, 28, 28, 34, 34, 34, 34, 34, 1, 1, 1, 1, 10, 27, 34, 34, 34, 34, 1] 34 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086718 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 14, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 34, 34, 34, 34, 14, 7, 1, 1, 1, 1, 34] 34 rigid atoms, others: [9, 10, 11, 12, 13, 14, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 30]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086718 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086718 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086718/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086718 Building REAL300000086719 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086719' /scratch/stefan/7769667/working/building/REAL300000086719 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086719 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086719/0 /scratch/stefan/7769667/working/building/REAL300000086719 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/748 `/scratch/stefan/7769667/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC=C(Br)CC2=CC=CC=C2)C=N1) `REAL300000086719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086719 none O=C([O-])C1=CC=C(N=NC=C(Br)CC2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'Br', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 17, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 83, 83, 83, 83, 83, 83, 1, 1, 1, 1, 22, 83, 83, 83, 83, 83, 83, 83, 1] 83 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086719 none O=C([O-])C1=CC=C(N=NC=C(Br)CC2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'Br', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 17, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 83, 83, 43, 43, 20, 20, 4, 20, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 20, 4, 4, 1, 1, 1, 1, 1, 83] 83 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086719 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086719 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086719/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086719 Building REAL300000086720 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086720' /scratch/stefan/7769667/working/building/REAL300000086720 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086720 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086720/0 /scratch/stefan/7769667/working/building/REAL300000086720 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/749 `/scratch/stefan/7769667/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC(=O)N2CCCC2)C=N1) `REAL300000086720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086720 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC(=O)N2CCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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: [2, 1, 2, 1, 1, 1, 1, 1, 7, 17, 17, 25, 25, 17, 25, 25, 25, 62, 170, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 7, 17, 25, 25, 25, 25, 170, 170, 201, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 45, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 695 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086720 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC(=O)N2CCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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: [201, 201, 201, 201, 201, 201, 126, 95, 95, 79, 79, 79, 79, 79, 79, 51, 14, 2, 1, 2, 1, 1, 1, 1, 1, 201, 201, 201, 201, 126, 95, 79, 79, 79, 78, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45]) total number of confs: 470 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086720 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC(=O)N2CCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 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: [25, 25, 25, 25, 25, 25, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 37, 67, 67, 79, 79, 79, 79, 25, 25, 25, 25, 13, 4, 1, 1, 1, 1, 37, 37, 79, 79, 79, 79, 79, 79, 79, 79, 25] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 296 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086720 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086720 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086720/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086720 Building REAL300000086721 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086721' /scratch/stefan/7769667/working/building/REAL300000086721 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086721 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086721/0 /scratch/stefan/7769667/working/building/REAL300000086721 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/750 `/scratch/stefan/7769667/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1) `REAL300000086721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086721 none CCCCCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [193, 187, 155, 119, 29, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 55, 55, 29, 55, 55, 201, 201, 201, 201, 201, 193, 192, 160, 160, 119, 119, 7, 1, 1, 1, 55, 55, 49, 55, 55] 201 rigid atoms, others: [35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 1109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086721 none CCCCCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [69, 55, 37, 28, 4, 1, 4, 4, 17, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 57, 57, 40, 40, 28, 28, 17, 55, 55, 55, 1, 1, 1, 1, 1] 201 rigid atoms, others: [5, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 488 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086721 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086721 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086721/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086721 Building REAL300000086722 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086722' /scratch/stefan/7769667/working/building/REAL300000086722 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086722 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086722/0 /scratch/stefan/7769667/working/building/REAL300000086722 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/751 `/scratch/stefan/7769667/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1) `REAL300000086722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086722 none CCCCCCCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [190, 181, 164, 130, 110, 84, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 42, 42, 24, 42, 42, 201, 201, 201, 201, 201, 194, 194, 170, 170, 133, 134, 111, 111, 84, 84, 7, 1, 1, 1, 42, 42, 38, 42, 42] 201 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 1115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086722 none CCCCCCCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [72, 66, 57, 41, 30, 23, 4, 1, 4, 4, 14, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 73, 72, 62, 62, 42, 42, 31, 31, 23, 23, 14, 42, 42, 42, 1, 1, 1, 1, 1] 201 rigid atoms, others: [7, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 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, 43]) total number of confs: 525 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086722 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086722 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086722/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086722 Building REAL300000086723 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086723' /scratch/stefan/7769667/working/building/REAL300000086723 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086723 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086723/0 /scratch/stefan/7769667/working/building/REAL300000086723 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/752 `/scratch/stefan/7769667/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC2=C1OCO2) `REAL300000086723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086723 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC2=C1OCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 7, 3, 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: [4, 1, 1, 1, 1, 1, 12, 12, 55, 144, 144, 143, 144, 144, 144, 144, 144, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 12, 55, 144, 144, 144, 1, 1, 1] 144 rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 34, 17, 18, 19, 20, 21, 22, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086723 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC2=C1OCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 144, 79, 79, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 79, 13, 1, 1, 1, 144, 144, 144] 144 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086723 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086723 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086723/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086723 Building REAL300000086724 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086724' /scratch/stefan/7769667/working/building/REAL300000086724 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086724 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086724/0 /scratch/stefan/7769667/working/building/REAL300000086724 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/753 `/scratch/stefan/7769667/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1) `REAL300000086724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086724 none CSC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 14, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 63, 152, 152, 152, 152, 152, 152, 152, 152, 1, 1, 7, 7, 7, 1, 1, 13, 13, 13, 63, 152, 152, 152, 1, 1] 162 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 34, 19, 20, 24, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 297 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086724 none CSC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 14, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [159, 65, 65, 152, 152, 65, 65, 65, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 152, 152, 162, 159, 161, 152, 152, 65, 65, 65, 13, 1, 1, 1, 152, 152] 162 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 555 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086724 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086724 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086724/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086724 Building REAL300000086725 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086725' /scratch/stefan/7769667/working/building/REAL300000086725 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086725 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086725/0 /scratch/stefan/7769667/working/building/REAL300000086725 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/754 `/scratch/stefan/7769667/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCN1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21) `REAL300000086725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086725 none CCCCCN1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [33, 19, 12, 6, 1, 1, 1, 1, 1, 1, 1, 5, 37, 37, 36, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 36, 38, 38, 37, 37, 19, 19, 14, 14, 6, 6, 5, 37, 37, 37, 1, 1, 1, 1] 201 rigid atoms, others: [43, 4, 5, 6, 7, 8, 9, 10, 23, 44, 20, 21, 22, 41, 24, 25, 42] set([0, 1, 2, 3, 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: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086725 none CCCCCN1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [197, 201, 145, 109, 37, 37, 36, 37, 37, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 197, 201, 201, 201, 201, 201, 201, 155, 155, 109, 109, 13, 1, 1, 1, 37, 37, 37, 37] 201 rigid atoms, others: [38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44]) total number of confs: 927 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086725 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086725 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086725/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086725 Building REAL300000086726 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086726' /scratch/stefan/7769667/working/building/REAL300000086726 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086726 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086726/0 /scratch/stefan/7769667/working/building/REAL300000086726 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/755 `/scratch/stefan/7769667/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(OC)=C1) `REAL300000086726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086726 none COC1=CC(OC)=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 5, 1, 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, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [2, 1, 1, 1, 1, 1, 3, 1, 1, 12, 12, 76, 165, 165, 165, 165, 165, 165, 165, 165, 1, 1, 3, 1, 3, 3, 3, 1, 3, 3, 3, 12, 75, 165, 165, 165, 4, 4, 4, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 39, 20, 21, 23, 27] set([0, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086726 none COC1=CC(OC)=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 5, 1, 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, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [197, 129, 86, 165, 165, 165, 184, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 165, 165, 186, 165, 196, 197, 197, 165, 184, 184, 184, 50, 11, 1, 1, 1, 186, 186, 186, 165] 201 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 646 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086726 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086726 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086726/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086726 Building REAL300000086727 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086727' /scratch/stefan/7769667/working/building/REAL300000086727 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086727 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086727/0 /scratch/stefan/7769667/working/building/REAL300000086727 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/756 `/scratch/stefan/7769667/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(=CN=NC1=CC=C(C(=O)[O-])N=C1)CC1=CC=CC=C1) `REAL300000086727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086727 none CCCCCC(=CN=NC1=CC=C(C(=O)[O-])N=C1)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 140, 110, 94, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 69, 79, 79, 79, 79, 79, 159, 159, 159, 159, 159, 144, 144, 110, 110, 94, 94, 26, 1, 1, 1, 69, 69, 79, 79, 79, 79, 79] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 911 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086727 none CCCCCC(=CN=NC1=CC=C(C(=O)[O-])N=C1)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 29, 23, 9, 4, 9, 9, 36, 36, 79, 79, 79, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 45, 45, 29, 29, 23, 23, 9, 79, 79, 79, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 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, 40, 41]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086727 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086727 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086727/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086727 Building REAL300000086728 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086728' /scratch/stefan/7769667/working/building/REAL300000086728 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086728 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086728/0 /scratch/stefan/7769667/working/building/REAL300000086728 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/757 `/scratch/stefan/7769667/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(N3CCOCC3)S2)C=N1) `REAL300000086728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086728 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3CCOCC3)S2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 14, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 46, 46, 63, 63, 63, 63, 123, 123, 123, 123, 123, 63, 1, 1, 1, 1, 10, 46, 63, 63, 123, 123, 123, 123, 123, 123, 123, 123, 1] 123 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 37] set([0, 2, 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086728 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3CCOCC3)S2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 14, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 123, 123, 123, 64, 33, 33, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 123, 123, 123, 123, 63, 33, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 123] 123 rigid atoms, others: [32, 33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37]) total number of confs: 264 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086728 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3CCOCC3)S2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 14, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 27, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 63, 63, 63, 63, 26, 8, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 63] 123 rigid atoms, others: [9, 10, 11, 12, 13, 14, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086728 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086728 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086728/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086728 Building REAL300000086729 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086729' /scratch/stefan/7769667/working/building/REAL300000086729 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086729 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086729/0 /scratch/stefan/7769667/working/building/REAL300000086729 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/758 `/scratch/stefan/7769667/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(Cl)C=C32)C=N1) `REAL300000086729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086729 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(Cl)C=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 12, 20, 20, 20, 20, 1] 21 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086729 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(Cl)C=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 7, 1, 1, 1, 1, 20] 21 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 29]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086729 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086729 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086729/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086729 Building REAL300000086730 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086730' /scratch/stefan/7769667/working/building/REAL300000086730 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086730 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086730/0 /scratch/stefan/7769667/working/building/REAL300000086730 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/759 `/scratch/stefan/7769667/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2)C(N2CCCC2)=C1C=NNC1=CC=C(C(=O)[O-])N=C1) `REAL300000086730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086730 none CC1=NN(C2=CC=CC=C2)C(N2CCCC2)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 108, 108, 109, 109, 109, 109, 109, 108, 108, 108, 108, 108, 108, 71, 71, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 109, 109, 109, 109, 109, 108, 108, 108, 108, 108, 108, 108, 108, 71, 12, 1, 1, 1] 109 rigid atoms, others: [47, 48, 49, 19, 20, 21, 22, 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, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 158 number of broken/clashed sets: 9 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086730 none CC1=NN(C2=CC=CC=C2)C(N2CCCC2)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 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, 1, 4, 4, 1, 4, 4, 1, 1, 2, 2, 2, 2, 1, 1, 7, 7, 41, 108, 108, 108, 108, 108, 108, 108, 108, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 7, 41, 108, 108, 108] 109 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 16, 17] set([5, 6, 7, 8, 9, 12, 13, 14, 15, 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]) total number of confs: 212 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: REAL300000086730 none CC1=NN(C2=CC=CC=C2)C(N2CCCC2)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 8, 8, 42, 108, 108, 108, 108, 108, 108, 108, 108, 2, 2, 2, 4, 4, 3, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 42, 108, 108, 108] 109 rigid atoms, others: [43, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48, 49]) total number of confs: 203 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086730 none CC1=NN(C2=CC=CC=C2)C(N2CCCC2)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 109 conformations in input total number of sets (complete confs): 109 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, 4, 4, 4, 4, 16, 16, 60, 109, 109, 109, 109, 109, 109, 109, 109, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 60, 109, 109, 109] 109 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36] set([0, 1, 2, 10, 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, 47, 48, 49]) total number of confs: 221 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086730 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086730 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086730/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086730 Building REAL300000086731 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086731' /scratch/stefan/7769667/working/building/REAL300000086731 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086731 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086731/0 /scratch/stefan/7769667/working/building/REAL300000086731 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/760 `/scratch/stefan/7769667/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C(C)C=C1) `REAL300000086731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086731 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 5, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 62, 172, 172, 172, 172, 172, 172, 172, 172, 1, 1, 1, 1, 4, 4, 1, 2, 4, 4, 2, 2, 2, 1, 11, 61, 172, 172, 172, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4] 172 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086731 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 5, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 22, 22, 89, 172, 172, 172, 172, 172, 172, 172, 172, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 22, 89, 172, 172, 172, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1] 172 rigid atoms, others: [38, 39, 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, 40, 41, 42]) total number of confs: 352 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086731 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 5, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 72, 72, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 72, 13, 1, 1, 1, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172] 172 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086731 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086731/1 /scratch/stefan/7769667/working/building/REAL300000086731 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/761 `/scratch/stefan/7769667/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C(C)C=C1) `REAL300000086731.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086731/1/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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086731 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 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, 1, 9, 68, 69, 161, 161, 161, 161, 161, 161, 161, 161, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 2, 2, 1, 9, 9, 161, 161, 161, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3] 161 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086731 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 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, 3, 3, 3, 3, 17, 92, 92, 161, 161, 161, 161, 161, 161, 161, 161, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 17, 17, 161, 161, 161, 3, 3, 3, 1, 1, 2, 2, 2, 1, 1] 161 rigid atoms, others: [38, 39, 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, 40, 41, 42]) total number of confs: 287 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086731 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 42, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 161, 161, 161, 161, 161, 161, 161, 161, 161, 161, 161, 161, 161, 161, 41, 42, 1, 1, 1, 161, 161, 161, 161, 161, 161, 161, 161, 161, 161] 161 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086731 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086731 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086731/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086731/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086731 Building REAL300000086732 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086732' /scratch/stefan/7769667/working/building/REAL300000086732 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086732 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086732/0 /scratch/stefan/7769667/working/building/REAL300000086732 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/762 `/scratch/stefan/7769667/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21) `REAL300000086732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086732 none CC(C)CN1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 1, 1, 1, 1, 1, 1, 1, 7, 34, 34, 33, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 34, 34, 34, 1, 1, 1, 1] 55 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 41, 39, 40, 19, 20, 21, 22, 23, 24, 38] set([0, 1, 2, 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: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086732 none CC(C)CN1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 34, 34, 33, 34, 34, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 55, 55, 55, 55, 55, 55, 55, 55, 55, 11, 1, 1, 1, 34, 34, 34, 34] 55 rigid atoms, others: [35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 176 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086732 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086732 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086732/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086732 Building REAL300000086733 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086733' /scratch/stefan/7769667/working/building/REAL300000086733 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086733 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086733/0 /scratch/stefan/7769667/working/building/REAL300000086733 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/763 `/scratch/stefan/7769667/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(OC(F)F)C=C2OC(F)F)C=N1) `REAL300000086733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086733 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC(F)F)C=C2OC(F)F)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 12, 5, 15, 15, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 6, 18, 18, 29, 29, 29, 29, 89, 132, 132, 29, 29, 29, 69, 123, 123, 1, 1, 1, 1, 6, 18, 29, 29, 132, 29, 123, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 683 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086733 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC(F)F)C=C2OC(F)F)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 12, 5, 15, 15, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 11, 4, 4, 1, 1, 1, 1, 1, 1, 11, 20, 20, 1, 1, 1, 7, 22, 22, 29, 29, 29, 29, 11, 4, 1, 1, 20, 1, 22, 29] 201 rigid atoms, others: [33, 9, 10, 11, 12, 13, 14, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 34, 35]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086733 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086733 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086733/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086733 Building REAL300000086734 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086734' /scratch/stefan/7769667/working/building/REAL300000086734 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086734 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086734/0 /scratch/stefan/7769667/working/building/REAL300000086734 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/764 `/scratch/stefan/7769667/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C(Cl)C=C1) `REAL300000086734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086734 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 67, 179, 179, 179, 179, 179, 179, 179, 179, 1, 1, 1, 1, 4, 4, 3, 4, 4, 4, 2, 2, 2, 1, 12, 66, 179, 179, 179, 2, 2, 2, 4, 4, 4, 4] 179 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086734 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 94, 179, 179, 179, 179, 179, 179, 179, 179, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 25, 94, 179, 179, 179, 4, 4, 4, 1, 1, 1, 1] 179 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]) total number of confs: 368 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086734 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 70, 70, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 70, 13, 1, 1, 1, 179, 179, 179, 179, 179, 179, 179] 179 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086734 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086734/1 /scratch/stefan/7769667/working/building/REAL300000086734 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/765 `/scratch/stefan/7769667/working/3D/765' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C(Cl)C=C1) `REAL300000086734.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086734/1/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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086734 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 67, 67, 158, 158, 158, 158, 158, 158, 158, 158, 1, 1, 1, 1, 3, 3, 2, 1, 3, 3, 2, 2, 2, 1, 9, 9, 158, 158, 158, 2, 2, 2, 3, 3, 3, 3] 158 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086734 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 17, 83, 83, 158, 158, 158, 158, 158, 158, 158, 158, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 17, 17, 158, 158, 158, 3, 3, 3, 1, 1, 1, 1] 158 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]) total number of confs: 284 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086734 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 42, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 158, 158, 158, 158, 158, 158, 158, 158, 158, 158, 41, 42, 1, 1, 1, 158, 158, 158, 158, 158, 158, 158] 158 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086734 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086734 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086734/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086734/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086734 Building REAL300000086735 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086735' /scratch/stefan/7769667/working/building/REAL300000086735 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086735 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086735/0 /scratch/stefan/7769667/working/building/REAL300000086735 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/766 `/scratch/stefan/7769667/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C(C)(C)C)C=C1) `REAL300000086735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086735 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C(C)(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [53, 54, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 68, 68, 54, 68, 82, 82, 82, 68, 68, 54, 54, 54, 12, 1, 1, 1, 68, 68, 82, 82, 82, 82, 82, 82, 82, 82, 82, 68, 68] 82 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 1, 2, 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, 41, 42]) total number of confs: 266 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086735 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C(C)(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 29, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 7, 7, 7, 29, 68, 68, 68, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 82 rigid atoms, others: [1, 41, 42, 13, 14, 15, 16, 17, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 136 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086735 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086735 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086735/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086735 Building REAL300000086736 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086736' /scratch/stefan/7769667/working/building/REAL300000086736 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086736 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086736/0 /scratch/stefan/7769667/working/building/REAL300000086736 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/767 `/scratch/stefan/7769667/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1OC(F)F) `REAL300000086736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086736 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [38, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 107, 107, 91, 107, 107, 107, 189, 201, 201, 39, 39, 39, 11, 1, 1, 1, 107, 107, 107, 107, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 432 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086736 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [7, 1, 7, 7, 33, 107, 107, 107, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 1, 1, 9, 37, 37, 7, 7, 7, 33, 107, 107, 107, 1, 1, 1, 1, 37] 201 rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 291 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086736 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086736 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086736/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086736 Building REAL300000086737 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086737' /scratch/stefan/7769667/working/building/REAL300000086737 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086737 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086737/0 /scratch/stefan/7769667/working/building/REAL300000086737 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/768 `/scratch/stefan/7769667/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(N2C(C)=CC(C=NNC3=CC=C(C(=O)[O-])N=C3)=C2C)C=C1) `REAL300000086737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086737 none COC1=CC=C(N2C(C)=CC(C=NNC3=CC=C(C(=O)[O-])N=C3)=C2C)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.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', '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, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 7, 7, 7, 7, 7, 30, 30, 96, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 30, 96, 201, 201, 201, 7, 7, 7, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 45, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086737 none COC1=CC=C(N2C(C)=CC(C=NNC3=CC=C(C(=O)[O-])N=C3)=C2C)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.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', '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, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 142, 142, 201, 201, 142, 142, 142, 142, 142, 63, 63, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 142, 142, 201, 201, 201, 201, 201, 201, 201, 142, 142, 142, 142, 63, 11, 1, 1, 1, 142, 142, 142, 201, 201] 201 rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45]) total number of confs: 617 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086737 none COC1=CC=C(N2C(C)=CC(C=NNC3=CC=C(C(=O)[O-])N=C3)=C2C)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.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', '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, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [7, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 43, 142, 142, 142, 142, 142, 142, 142, 142, 1, 1, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 1, 10, 43, 142, 142, 142, 2, 2, 2, 7, 7] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 23, 24] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086737 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086737/1 /scratch/stefan/7769667/working/building/REAL300000086737 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/769 `/scratch/stefan/7769667/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(N2C(C)=CC(CN=NC3=CC=C(C(=O)[O-])N=C3)=C2C)C=C1) `REAL300000086737.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086737/1/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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086737 none COC1=CC=C(N2C(C)=CC(CN=NC3=CC=C(C(=O)[O-])N=C3)=C2C)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.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', '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, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 5, 5, 5, 5, 5, 29, 131, 131, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 29, 29, 201, 201, 201, 5, 5, 5, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 45, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086737 none COC1=CC=C(N2C(C)=CC(CN=NC3=CC=C(C(=O)[O-])N=C3)=C2C)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.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', '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, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 189, 201, 201, 115, 115, 115, 115, 115, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 115, 115, 201, 201, 201, 201, 201, 201, 201, 115, 115, 115, 115, 26, 27, 1, 1, 1, 115, 115, 115, 201, 201] 201 rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45]) total number of confs: 426 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086737 none COC1=CC=C(N2C(C)=CC(CN=NC3=CC=C(C(=O)[O-])N=C3)=C2C)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.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', '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, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 2, 2, 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: [5, 4, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 53, 54, 115, 115, 115, 115, 115, 115, 115, 115, 1, 1, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 8, 8, 115, 115, 115, 2, 2, 2, 5, 5] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 23, 24] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086737 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086737 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086737/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086737/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086737 Building REAL300000086738 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086738' /scratch/stefan/7769667/working/building/REAL300000086738 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086738 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086738/0 /scratch/stefan/7769667/working/building/REAL300000086738 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/770 `/scratch/stefan/7769667/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)N2C=CSC2=N1) `REAL300000086738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086738 none CC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)N2C=CSC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 8, 1, 1, 14, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 10, 10, 28, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 28, 59, 59, 59, 1, 1] 59 rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 18, 19, 20, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086738 none CC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)N2C=CSC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 8, 1, 1, 14, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 43, 43, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 43, 13, 1, 1, 1, 59, 59] 59 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086738 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086738 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086738/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086738 Building REAL300000086739 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086739' /scratch/stefan/7769667/working/building/REAL300000086739 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086739 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086739/0 /scratch/stefan/7769667/working/building/REAL300000086739 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/771 `/scratch/stefan/7769667/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(=O)C1CC1) `REAL300000086739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086739 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 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] 0 hydrogens 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, 14, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 7, 17, 17, 57, 57, 3, 4, 4, 1, 6, 13, 31, 31, 31, 1, 1, 57, 57, 57, 57, 57] 201 rigid atoms, others: [1, 2, 3, 4, 5, 35, 17, 18, 19, 20, 36, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086739 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 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] 0 hydrogens 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, 57, 57, 57, 47, 57, 97, 97, 116, 201, 201, 201, 201, 201, 201, 201, 201, 57, 57, 33, 13, 1, 13, 1, 1, 1, 81, 81, 81, 57, 97, 116, 201, 201, 201, 57, 57, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 21, 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, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 570 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086739 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 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] 0 hydrogens 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, 31, 31, 31, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 87, 134, 134, 201, 201, 59, 59, 59, 31, 11, 7, 1, 1, 1, 31, 31, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 586 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086739 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086739 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086739/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086739 Building REAL300000086740 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086740' /scratch/stefan/7769667/working/building/REAL300000086740 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086740 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086740/0 /scratch/stefan/7769667/working/building/REAL300000086740 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/772 `/scratch/stefan/7769667/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC1=CC=C(F)C=C1) `REAL300000086740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086740 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', '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, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7] 0 hydrogens 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, 10, 18, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 9, 37, 67, 67, 37, 67, 67, 67, 4, 4, 4, 1, 6, 10, 19, 19, 19, 1, 1, 37, 37, 67, 67, 67, 67] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 38, 39, 17, 18, 19, 20] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086740 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', '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, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7] 0 hydrogens 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, 67, 67, 67, 31, 67, 94, 94, 117, 201, 201, 201, 201, 201, 201, 201, 201, 67, 67, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 67, 94, 117, 201, 201, 201, 67, 67, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 21, 22, 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, 19, 20, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 626 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086740 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', '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, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7] 0 hydrogens 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, 19, 19, 19, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 80, 169, 201, 201, 169, 201, 201, 201, 35, 35, 35, 19, 8, 4, 1, 1, 1, 19, 19, 169, 169, 201, 201, 201, 201] 201 rigid atoms, others: [35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 736 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086740 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086740 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086740/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086740 Building REAL300000086741 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086741' /scratch/stefan/7769667/working/building/REAL300000086741 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086741 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086741/0 /scratch/stefan/7769667/working/building/REAL300000086741 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/773 `/scratch/stefan/7769667/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NC2=CC=CC(C=NNC3=CC=C(C(=O)[O-])N=C3)=C2)C=C1) `REAL300000086741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086741 none COC1=CC=C(C(=O)NC2=CC=CC(C=NNC3=CC=C(C(=O)[O-])N=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 5, 5, 5, 21, 21, 21, 21, 21, 60, 60, 108, 201, 201, 201, 201, 201, 201, 201, 201, 21, 1, 1, 1, 1, 1, 1, 1, 5, 21, 21, 21, 60, 108, 201, 201, 201, 21, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 44, 45, 33, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 464 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086741 none COC1=CC=C(C(=O)NC2=CC=CC(C=NNC3=CC=C(C(=O)[O-])N=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 136, 136, 136, 70, 70, 70, 70, 70, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 201, 201, 201, 201, 201, 201, 201, 136, 70, 70, 70, 30, 8, 1, 1, 1, 70, 201, 201] 201 rigid atoms, others: [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, 38, 39, 43, 44, 45]) total number of confs: 439 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086741 none COC1=CC=C(C(=O)NC2=CC=CC(C=NNC3=CC=C(C(=O)[O-])N=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 70, 70, 70, 70, 69, 70, 70, 70, 1, 21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 6, 22, 70, 70, 70, 1, 21, 21] 201 rigid atoms, others: [35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 157 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086741 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086741 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086741/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086741 Building REAL300000086742 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086742' /scratch/stefan/7769667/working/building/REAL300000086742 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086742 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086742/0 /scratch/stefan/7769667/working/building/REAL300000086742 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/774 `/scratch/stefan/7769667/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(NC(=O)C3=CC=CC=C3Cl)=C2)C=N1) `REAL300000086742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086742 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(NC(=O)C3=CC=CC=C3Cl)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [2, 1, 2, 1, 1, 1, 1, 1, 6, 23, 23, 46, 46, 46, 46, 46, 104, 104, 104, 201, 201, 201, 201, 201, 201, 46, 1, 1, 1, 1, 6, 23, 46, 46, 46, 104, 201, 201, 201, 201, 46, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086742 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(NC(=O)C3=CC=CC=C3Cl)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [201, 201, 201, 201, 201, 201, 108, 54, 54, 24, 24, 24, 24, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 24, 201, 201, 201, 201, 108, 54, 24, 24, 24, 7, 1, 1, 1, 1, 24, 201] 201 rigid atoms, others: [36, 37, 38, 39, 16, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 464 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086742 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(NC(=O)C3=CC=CC=C3Cl)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [47, 46, 47, 46, 46, 46, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 24, 24, 20, 24, 24, 24, 1, 46, 46, 46, 46, 19, 6, 1, 1, 1, 8, 24, 24, 24, 24, 1, 46] 201 rigid atoms, others: [32, 33, 34, 40, 9, 10, 11, 12, 13, 14, 15, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 41]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086742 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086742 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086742/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086742 Building REAL300000086743 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086743' /scratch/stefan/7769667/working/building/REAL300000086743 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086743 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086743/0 /scratch/stefan/7769667/working/building/REAL300000086743 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/775 `/scratch/stefan/7769667/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(=O)C1=CC=NC=C1) `REAL300000086743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086743 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(=O)C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 7, 5, 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, 7, 7, 21, 57, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 7, 25, 25, 45, 45, 25, 45, 45, 3, 3, 3, 1, 7, 21, 58, 58, 58, 1, 1, 45, 45, 45, 45] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 38, 39, 17, 18, 19, 20] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086743 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(=O)C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 7, 5, 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: [75, 45, 45, 45, 30, 45, 82, 82, 124, 201, 201, 201, 201, 201, 201, 201, 201, 45, 45, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 75, 75, 75, 45, 82, 124, 201, 201, 201, 45, 45, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 21, 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, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 593 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086743 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(=O)C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 7, 5, 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: [91, 58, 58, 58, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 146, 197, 197, 201, 201, 197, 201, 201, 91, 91, 91, 58, 24, 7, 1, 1, 1, 58, 58, 201, 201, 201, 201] 201 rigid atoms, others: [35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 475 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086743 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086743 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086743/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086743 Building REAL300000086744 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086744' /scratch/stefan/7769667/working/building/REAL300000086744 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086744 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086744/0 /scratch/stefan/7769667/working/building/REAL300000086744 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/776 `/scratch/stefan/7769667/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC3=CC=CC=C3N=C2Cl)C=N1) `REAL300000086744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086744 none O=C([O-])C1=CC=C(NN=CC2=CC3=CC=CC=C3N=C2Cl)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 11, 29, 29, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 11, 29, 39, 39, 39, 39, 39, 1] 39 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086744 none O=C([O-])C1=CC=C(NN=CC2=CC3=CC=CC=C3N=C2Cl)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 18, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 18, 8, 1, 1, 1, 1, 1, 39] 39 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24, 25, 26]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086744 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086744 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086744/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086744 Building REAL300000086745 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086745' /scratch/stefan/7769667/working/building/REAL300000086745 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086745 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086745/0 /scratch/stefan/7769667/working/building/REAL300000086745 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/777 `/scratch/stefan/7769667/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C(=O)NC3=C(Br)C=C(F)C=C23)C=N1) `REAL300000086745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086745 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=C(Br)C=C(F)C=C23)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 17, 1, 1, 15, 1, 1, 1, 8, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 12, 20, 20, 20, 1] 21 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086745 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=C(Br)C=C(F)C=C23)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 17, 1, 1, 15, 1, 1, 1, 8, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 7, 1, 1, 1, 20] 21 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 29]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086745 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086745 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086745/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086745 Building REAL300000086746 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086746' /scratch/stefan/7769667/working/building/REAL300000086746 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086746 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086746/0 /scratch/stefan/7769667/working/building/REAL300000086746 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/778 `/scratch/stefan/7769667/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(F)C=C32)C=N1) `REAL300000086746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086746 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(F)C=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 12, 20, 20, 20, 20, 1] 21 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086746 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(F)C=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 7, 1, 1, 1, 1, 20] 21 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 29]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086746 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086746 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086746/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086746 Building REAL300000086747 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086747' /scratch/stefan/7769667/working/building/REAL300000086747 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086747 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086747/0 /scratch/stefan/7769667/working/building/REAL300000086747 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/779 `/scratch/stefan/7769667/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCCN1C=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(C2=CC=CC=C2)=N1) `REAL300000086747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086747 none N#CCCN1C=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [18, 18, 8, 1, 1, 1, 1, 1, 8, 8, 23, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 6, 6, 1, 6, 6, 1, 18, 18, 8, 8, 1, 8, 23, 56, 56, 56, 6, 6, 1, 6, 6] 201 rigid atoms, others: [3, 4, 5, 6, 7, 19, 20, 26, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086747 none N#CCCN1C=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [40, 40, 22, 6, 6, 6, 6, 6, 13, 13, 35, 79, 79, 79, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 1, 1, 6, 40, 40, 22, 22, 6, 13, 35, 79, 79, 79, 1, 1, 1, 1, 1] 201 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]) total number of confs: 317 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086747 none N#CCCN1C=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 157, 56, 56, 56, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 79, 79, 57, 79, 79, 56, 201, 201, 157, 157, 56, 34, 8, 1, 1, 1, 79, 79, 56, 79, 79] 201 rigid atoms, others: [34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 862 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086747 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086747 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086747/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086747 Building REAL300000086748 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086748' /scratch/stefan/7769667/working/building/REAL300000086748 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086748 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086748/0 /scratch/stefan/7769667/working/building/REAL300000086748 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/780 `/scratch/stefan/7769667/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC2=CC(C=NNC3=CC=C(C(=O)[O-])N=C3)=C(Cl)N=C12) `REAL300000086748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086748 none CC1=CC=CC2=CC(C=NNC3=CC=C(C(=O)[O-])N=C3)=C(Cl)N=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 16, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 3, 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, 8, 8, 22, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 8, 22, 41, 41, 41] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 27, 28, 29, 30] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 31]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086748 none CC1=CC=CC2=CC(C=NNC3=CC=C(C(=O)[O-])N=C3)=C(Cl)N=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 16, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 33, 33, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 33, 10, 1, 1, 1] 41 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086748 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086748 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086748/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086748 Building REAL300000086749 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086749' /scratch/stefan/7769667/working/building/REAL300000086749 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086749 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086749/0 /scratch/stefan/7769667/working/building/REAL300000086749 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/781 `/scratch/stefan/7769667/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Br)C=C1) `REAL300000086749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086749 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [38, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 48, 48, 39, 39, 48, 48, 39, 39, 39, 11, 1, 1, 1, 48, 48, 48, 48] 48 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086749 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 16, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 48, 48, 48, 1, 1, 1, 1] 48 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 86 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086749 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086749 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086749/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086749 Building REAL300000086750 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086750' /scratch/stefan/7769667/working/building/REAL300000086750 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086750 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086750/0 /scratch/stefan/7769667/working/building/REAL300000086750 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/782 `/scratch/stefan/7769667/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(Br)=C1) `REAL300000086750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086750 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [62, 63, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 105, 105, 105, 105, 105, 105, 63, 63, 63, 13, 1, 1, 1, 105, 105, 105, 105] 105 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086750 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 51, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 51, 105, 105, 105, 1, 1, 1, 1] 105 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 209 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086750 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086750 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086750/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086750 Building REAL300000086751 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086751' /scratch/stefan/7769667/working/building/REAL300000086751 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086751 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086751/0 /scratch/stefan/7769667/working/building/REAL300000086751 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/783 `/scratch/stefan/7769667/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C(OC)=C1) `REAL300000086751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086751 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 5, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 65, 184, 184, 184, 184, 184, 184, 184, 184, 1, 1, 3, 1, 3, 3, 3, 1, 1, 13, 13, 13, 65, 184, 184, 184, 3, 3, 3, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 38, 19, 20, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 333 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086751 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 5, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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: [199, 184, 151, 184, 184, 59, 59, 58, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 184, 184, 201, 184, 199, 199, 199, 184, 184, 59, 59, 59, 11, 1, 1, 1, 201, 201, 201, 184] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 455 number of broken/clashed sets: 77 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086751 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086751 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086751/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086751 Building REAL300000086752 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086752' /scratch/stefan/7769667/working/building/REAL300000086752 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086752 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086752/0 /scratch/stefan/7769667/working/building/REAL300000086752 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/784 `/scratch/stefan/7769667/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC2=CC=CC=C21) `REAL300000086752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086752 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [53, 54, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 102, 102, 102, 102, 102, 102, 102, 102, 102, 54, 54, 54, 13, 1, 1, 1, 102, 102, 102, 102, 102, 102, 102] 102 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 165 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086752 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 40, 102, 102, 102, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 40, 102, 102, 102, 1, 1, 1, 1, 1, 1, 1] 102 rigid atoms, others: [32, 1, 34, 35, 36, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 192 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086752 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086752 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086752/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086752 Building REAL300000086753 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086753' /scratch/stefan/7769667/working/building/REAL300000086753 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086753 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086753/0 /scratch/stefan/7769667/working/building/REAL300000086753 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/785 `/scratch/stefan/7769667/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C3=CC=CC=C3C3=CC=CC=C32)C=N1) `REAL300000086753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086753 none O=C([O-])C1=CC=C(NN=C2C3=CC=CC=C3C3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 34 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086753 none O=C([O-])C1=CC=C(NN=C2C3=CC=CC=C3C3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 17] 17 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 6, 35, 22, 23, 24, 25, 26]) total number of confs: 29 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086753 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086753 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086753/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086753 Building REAL300000086754 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086754' /scratch/stefan/7769667/working/building/REAL300000086754 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086754 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086754/0 /scratch/stefan/7769667/working/building/REAL300000086754 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/786 `/scratch/stefan/7769667/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCCCCCCCCCC2)C=N1) `REAL300000086754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086754 none O=C([O-])C1=CC=C(N=NC2CCCCCCCCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1] 11 rigid atoms, others: [1, 3, 4, 5, 6, 7, 48, 21, 22, 23, 24] set([0, 2, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086754 none O=C([O-])C1=CC=C(N=NC2CCCCCCCCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 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, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11] 11 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 48, 21, 22, 23, 24]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086754 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086754 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086754/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086754 Building REAL300000086755 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086755' /scratch/stefan/7769667/working/building/REAL300000086755 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086755 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086755/0 /scratch/stefan/7769667/working/building/REAL300000086755 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/787 `/scratch/stefan/7769667/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C([N+](=O)[O-])C=C1) `REAL300000086755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086755 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C([N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [38, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 49, 49, 39, 39, 49, 49, 49, 49, 39, 39, 39, 11, 1, 1, 1, 49, 49, 49, 49] 49 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28] set([0, 1, 2, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086755 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C([N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 16, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 2, 2, 1, 1, 6, 6, 6, 16, 49, 49, 49, 1, 1, 1, 1] 49 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 91 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086755 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086755 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086755/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086755 Building REAL300000086756 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086756' /scratch/stefan/7769667/working/building/REAL300000086756 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086756 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086756/0 /scratch/stefan/7769667/working/building/REAL300000086756 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/788 `/scratch/stefan/7769667/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC=C2O)C=N1) `REAL300000086756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086756 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC=C2O)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 36, 36, 43, 43, 43, 40, 43, 43, 43, 1, 1, 1, 1, 12, 36, 43, 43, 43, 86, 1] 86 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27]) total number of confs: 172 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086756 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC=C2O)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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: [43, 43, 43, 43, 43, 43, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 26, 8, 1, 1, 1, 2, 43] 86 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 87 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086756 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086756 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086756/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086756 Building REAL300000086757 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086757' /scratch/stefan/7769667/working/building/REAL300000086757 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086757 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086757/0 /scratch/stefan/7769667/working/building/REAL300000086757 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/789 `/scratch/stefan/7769667/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(OC)=C1) `REAL300000086757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086757 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(OC)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 5, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 13, 13, 50, 134, 134, 134, 134, 134, 134, 134, 134, 1, 1, 3, 1, 2, 2, 2, 1, 1, 13, 50, 134, 134, 134, 4, 4, 4, 1] 157 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 21, 25, 26, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086757 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(OC)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 5, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [153, 134, 78, 134, 133, 68, 68, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 134, 134, 156, 134, 153, 153, 153, 134, 134, 68, 13, 1, 1, 1, 156, 156, 156, 134] 157 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 517 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086757 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086757 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086757/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086757 Building REAL300000086758 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086758' /scratch/stefan/7769667/working/building/REAL300000086758 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086758 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086758/0 /scratch/stefan/7769667/working/building/REAL300000086758 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/790 `/scratch/stefan/7769667/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=C(C)N(C2=CC=CC=C2)N=C1) `REAL300000086758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086758 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=C(C)N(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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, 11, 11, 8, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [65, 66, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 66, 66, 66, 13, 1, 1, 1, 145, 145, 145, 145, 145, 145, 145, 145, 145] 145 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 219 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: REAL300000086758 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=C(C)N(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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, 11, 11, 8, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [19, 3, 19, 19, 71, 145, 145, 145, 145, 145, 145, 145, 145, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 19, 71, 145, 145, 145, 3, 3, 3, 1, 1, 1, 1, 1, 3] 145 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]) total number of confs: 305 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086758 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=C(C)N(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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, 11, 11, 8, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 60, 145, 145, 145, 145, 145, 145, 145, 145, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 10, 10, 10, 60, 145, 145, 145, 2, 2, 2, 3, 3, 2, 3, 3, 1] 145 rigid atoms, others: [1, 40, 13, 14, 15, 16, 17, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 285 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086758 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086758 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086758/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086758 Building REAL300000086759 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086759' /scratch/stefan/7769667/working/building/REAL300000086759 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086759 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086759/0 /scratch/stefan/7769667/working/building/REAL300000086759 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/791 `/scratch/stefan/7769667/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC(Br)=CC=C32)C=N1) `REAL300000086759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086759 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC(Br)=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 1, 8, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 8, 14, 14, 14, 14, 1] 15 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086759 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC(Br)=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 1, 8, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 15, 14, 14, 14, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 7, 1, 1, 1, 1, 14] 15 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 29]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086759 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086759 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086759/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086759 Building REAL300000086760 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086760' /scratch/stefan/7769667/working/building/REAL300000086760 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086760 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086760/0 /scratch/stefan/7769667/working/building/REAL300000086760 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/792 `/scratch/stefan/7769667/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(Cl)=C2Cl)C=N1) `REAL300000086760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086760 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(Cl)=C2Cl)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 11, 35, 35, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 11, 35, 45, 45, 45, 1] 45 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086760 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(Cl)=C2Cl)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 45, 22, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 22, 10, 1, 1, 1, 45] 45 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086760 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086760 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086760/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086760 Building REAL300000086761 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086761' /scratch/stefan/7769667/working/building/REAL300000086761 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086761 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086761/0 /scratch/stefan/7769667/working/building/REAL300000086761 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/793 `/scratch/stefan/7769667/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(Cl)C(Cl)=C2)C=N1) `REAL300000086761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086761 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Cl)C(Cl)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 11, 35, 35, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 11, 35, 69, 69, 69, 1] 69 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086761 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Cl)C(Cl)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 69, 69, 33, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 33, 11, 1, 1, 1, 69] 69 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086761 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086761 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086761/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086761 Building REAL300000086762 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086762' /scratch/stefan/7769667/working/building/REAL300000086762 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086762 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086762/0 /scratch/stefan/7769667/working/building/REAL300000086762 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/794 `/scratch/stefan/7769667/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=C(O)C2=CC=CC=C2C=C1) `REAL300000086762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086762 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=C(O)C2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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] 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: [50, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 51, 51, 51, 11, 1, 1, 1, 154, 77, 77, 77, 77, 77, 77] 154 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 282 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086762 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=C(O)C2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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] 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: [11, 1, 11, 11, 31, 77, 77, 77, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 31, 77, 77, 77, 2, 1, 1, 1, 1, 1, 1] 154 rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 153 number of broken/clashed sets: 86 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086762 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086762 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086762/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086762 Building REAL300000086763 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086763' /scratch/stefan/7769667/working/building/REAL300000086763 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086763 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086763/0 /scratch/stefan/7769667/working/building/REAL300000086763 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/795 `/scratch/stefan/7769667/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C([N+](=O)[O-])=C1) `REAL300000086763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086763 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [56, 57, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 119, 119, 79, 119, 119, 119, 119, 119, 119, 57, 57, 57, 13, 1, 1, 1, 119, 119, 119] 119 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 1, 2, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 342 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086763 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 51, 119, 119, 119, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 51, 119, 119, 119, 1, 1, 1] 119 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 19, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 239 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086763 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086763 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086763/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086763 Building REAL300000086764 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086764' /scratch/stefan/7769667/working/building/REAL300000086764 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086764 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086764/0 /scratch/stefan/7769667/working/building/REAL300000086764 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/796 `/scratch/stefan/7769667/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC1=CC=CC=C1)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1) `REAL300000086764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086764 none CCN(CC1=CC=CC=C1)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [32, 14, 3, 1, 1, 1, 1, 1, 1, 1, 14, 25, 25, 15, 20, 77, 77, 115, 195, 195, 195, 195, 195, 195, 195, 195, 25, 25, 33, 33, 33, 32, 32, 3, 3, 1, 1, 1, 1, 1, 25, 25, 76, 115, 195, 195, 195, 25, 25] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 39, 35, 36, 38, 37] set([0, 1, 2, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 612 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: REAL300000086764 none CCN(CC1=CC=CC=C1)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [123, 63, 17, 63, 179, 195, 195, 179, 195, 195, 17, 33, 33, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 123, 123, 123, 123, 123, 179, 179, 195, 195, 179, 195, 195, 33, 33, 11, 7, 1, 1, 1, 33, 33] 201 rigid atoms, others: [44, 45, 46, 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, 38, 39, 40, 41, 42, 43, 47, 48]) total number of confs: 1081 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086764 none CCN(CC1=CC=CC=C1)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 5, 1, 5, 21, 25, 25, 21, 25, 25, 1, 1, 1, 1, 1, 6, 6, 14, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 19, 19, 19, 19, 19, 21, 21, 25, 25, 21, 25, 25, 1, 1, 6, 14, 33, 33, 33, 1, 1] 201 rigid atoms, others: [2, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 218 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086764 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086764 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086764/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086764 Building REAL300000086765 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086765' /scratch/stefan/7769667/working/building/REAL300000086765 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086765 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086765/0 /scratch/stefan/7769667/working/building/REAL300000086765 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/797 `/scratch/stefan/7769667/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(OC(F)F)C=C2)C=N1) `REAL300000086765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086765 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC(F)F)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 10, 54, 54, 81, 81, 54, 54, 179, 201, 201, 81, 81, 1, 1, 1, 1, 10, 54, 81, 81, 201, 81, 81, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 487 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086765 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC(F)F)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 82, 81, 23, 3, 3, 1, 1, 1, 1, 1, 1, 12, 41, 41, 1, 1, 82, 82, 82, 81, 23, 3, 1, 1, 41, 1, 1, 81] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 18, 19, 26, 27, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 28, 31]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086765 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086765 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086765/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086765 Building REAL300000086766 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086766' /scratch/stefan/7769667/working/building/REAL300000086766 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086766 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086766/0 /scratch/stefan/7769667/working/building/REAL300000086766 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/798 `/scratch/stefan/7769667/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C3C=CC=CC3=C(Cl)C3=CC=CC=C32)C=N1) `REAL300000086766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086766 none O=C([O-])C1=CC=C(NN=CC2=C3C=CC=CC3=C(Cl)C3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 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] 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, 2, 1, 1, 1, 1, 1, 12, 44, 44, 65, 65, 65, 65, 65, 65, 44, 44, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 12, 44, 65, 65, 65, 65, 65, 65, 65, 65, 1] 65 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086766 none O=C([O-])C1=CC=C(NN=CC2=C3C=CC=CC3=C(Cl)C3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 65, 65, 32, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 32, 10, 1, 1, 1, 1, 1, 1, 1, 1, 65] 65 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 25, 26, 27, 28, 29, 30]) total number of confs: 128 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086766 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086766 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086766/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086766 Building REAL300000086767 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086767' /scratch/stefan/7769667/working/building/REAL300000086767 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086767 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086767/0 /scratch/stefan/7769667/working/building/REAL300000086767 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/799 `/scratch/stefan/7769667/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2C(F)(F)F)C=N1) `REAL300000086767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086767 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2C(F)(F)F)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 11, 46, 46, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 11, 46, 58, 58, 58, 58, 1] 58 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086767 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2C(F)(F)F)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 58, 58, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 58, 58, 58, 58, 31, 7, 1, 1, 1, 1, 58] 58 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086767 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086767 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086767/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086767 Building REAL300000086768 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086768' /scratch/stefan/7769667/working/building/REAL300000086768 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086768 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086768/0 /scratch/stefan/7769667/working/building/REAL300000086768 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/800 `/scratch/stefan/7769667/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1) `REAL300000086768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086768 none CCCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 8, 3, 1, 1, 1, 1, 1, 1, 6, 6, 26, 68, 68, 67, 68, 68, 68, 68, 68, 1, 1, 33, 33, 33, 32, 32, 20, 20, 8, 8, 1, 1, 6, 26, 68, 68, 68, 1, 1] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 39, 40, 21, 22] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 286 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086768 none CCCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 125, 108, 55, 30, 68, 68, 30, 30, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68, 201, 201, 201, 201, 201, 201, 201, 123, 123, 68, 68, 30, 7, 1, 1, 1, 68, 68] 201 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 811 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086768 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086768 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086768/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086768 Building REAL300000086769 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086769' /scratch/stefan/7769667/working/building/REAL300000086769 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086769 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086769/0 /scratch/stefan/7769667/working/building/REAL300000086769 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/801 `/scratch/stefan/7769667/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1) `REAL300000086769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086769 none CC(C)CCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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: [21, 16, 21, 9, 3, 1, 1, 1, 1, 1, 1, 6, 6, 35, 87, 87, 86, 87, 87, 87, 87, 87, 1, 1, 21, 21, 21, 21, 21, 21, 21, 16, 16, 9, 9, 1, 1, 6, 35, 87, 87, 87, 1, 1] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 43, 22, 23, 42] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 263 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086769 none CC(C)CCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 158, 122, 65, 41, 87, 87, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 87, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 152, 87, 87, 41, 11, 1, 1, 1, 87, 87] 201 rigid atoms, others: [39, 40, 41, 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, 33, 34, 35, 36, 37, 38, 42, 43]) total number of confs: 801 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086769 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086769 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086769/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086769 Building REAL300000086770 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086770' /scratch/stefan/7769667/working/building/REAL300000086770 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086770 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086770/0 /scratch/stefan/7769667/working/building/REAL300000086770 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/802 `/scratch/stefan/7769667/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(OC3=CC=CC=C3)=C2)C=N1) `REAL300000086770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086770 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(OC3=CC=CC=C3)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 6, 24, 24, 59, 59, 58, 59, 59, 180, 201, 201, 201, 201, 201, 59, 1, 1, 1, 1, 6, 24, 59, 59, 58, 201, 201, 201, 201, 201, 59, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 23, 24, 25, 26, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086770 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(OC3=CC=CC=C3)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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: [201, 201, 201, 201, 201, 201, 106, 57, 57, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 17, 201, 201, 201, 201, 106, 57, 17, 17, 17, 1, 1, 1, 1, 1, 17, 201] 201 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: 448 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086770 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(OC3=CC=CC=C3)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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: [59, 59, 59, 59, 59, 59, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 9, 17, 17, 10, 17, 17, 1, 59, 59, 59, 59, 24, 7, 1, 1, 1, 17, 17, 17, 17, 17, 1, 59] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 38]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086770 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086770 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086770/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086770 Building REAL300000086771 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086771' /scratch/stefan/7769667/working/building/REAL300000086771 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086771 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086771/0 /scratch/stefan/7769667/working/building/REAL300000086771 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/803 `/scratch/stefan/7769667/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(OCCC)=C1) `REAL300000086771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086771 none CCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 5, 5, 5, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [16, 8, 6, 1, 1, 1, 1, 1, 1, 4, 4, 8, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 7, 18, 30, 1, 17, 17, 17, 16, 16, 8, 8, 1, 1, 4, 8, 16, 16, 16, 18, 18, 30, 30, 30, 30, 30, 1] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 47, 20, 21, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086771 none CCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 5, 5, 5, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [107, 49, 46, 16, 16, 16, 16, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 49, 79, 115, 16, 107, 107, 107, 107, 107, 49, 49, 16, 16, 10, 6, 1, 1, 1, 79, 79, 115, 115, 115, 115, 115, 16] 201 rigid atoms, others: [37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 749 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086771 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086771 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086771/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086771 Building REAL300000086772 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086772' /scratch/stefan/7769667/working/building/REAL300000086772 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086772 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086772/0 /scratch/stefan/7769667/working/building/REAL300000086772 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/804 `/scratch/stefan/7769667/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(O)=C1) `REAL300000086772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086772 none CCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 246 conformations in input total number of sets (complete confs): 246 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 1, 1, 1, 1, 1, 1, 8, 8, 30, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1, 1, 16, 16, 16, 16, 16, 1, 1, 8, 30, 81, 81, 81, 2, 1] 246 rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 19, 20, 21, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 184 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086772 none CCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 246 conformations in input total number of sets (complete confs): 246 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 81, 58, 81, 81, 55, 55, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 123, 123, 123, 123, 123, 81, 81, 55, 12, 1, 1, 1, 162, 81] 246 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 472 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086772 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086772 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086772/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086772 Building REAL300000086773 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086773' /scratch/stefan/7769667/working/building/REAL300000086773 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086773 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086773/0 /scratch/stefan/7769667/working/building/REAL300000086773 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/805 `/scratch/stefan/7769667/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC([N+](=O)[O-])=C2[O-])C=N1) `REAL300000086773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086773 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC([N+](=O)[O-])=C2[O-])C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 1, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 18, 18, 19, 19, 19, 18, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 11, 18, 19, 19, 1] 19 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086773 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC([N+](=O)[O-])=C2[O-])C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 1, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 3, 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, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 9, 4, 1, 1, 19] 19 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086773 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086773 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086773/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086773 Building REAL300000086774 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086774' /scratch/stefan/7769667/working/building/REAL300000086774 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086774 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086774/0 /scratch/stefan/7769667/working/building/REAL300000086774 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/806 `/scratch/stefan/7769667/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2I)C=N1) `REAL300000086774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086774 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2I)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 18, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 13, 45, 45, 61, 61, 45, 61, 61, 61, 1, 1, 1, 1, 13, 45, 61, 61, 58, 61, 1] 61 rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086774 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2I)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 18, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 61, 61, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 33, 8, 1, 1, 1, 1, 61] 61 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 27]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086774 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086774 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086774/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086774 Building REAL300000086775 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086775' /scratch/stefan/7769667/working/building/REAL300000086775 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086775 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086775/0 /scratch/stefan/7769667/working/building/REAL300000086775 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/807 `/scratch/stefan/7769667/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C(O)=C1) `REAL300000086775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086775 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'O.3', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 344 conformations in input total number of sets (complete confs): 344 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 66, 172, 172, 172, 172, 172, 172, 172, 172, 1, 1, 1, 3, 3, 3, 1, 1, 13, 13, 13, 66, 172, 172, 172, 2, 1] 344 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 25, 26, 35] set([0, 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: 325 number of broken/clashed sets: 196 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086775 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'O.3', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 344 conformations in input total number of sets (complete confs): 344 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 154, 172, 172, 60, 60, 60, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 172, 172, 172, 172, 60, 60, 60, 11, 1, 1, 1, 344, 172] 344 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 672 number of broken/clashed sets: 196 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086775 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086775 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086775/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086775 Building REAL300000086776 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086776' /scratch/stefan/7769667/working/building/REAL300000086776 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086776 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086776/0 /scratch/stefan/7769667/working/building/REAL300000086776 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/808 `/scratch/stefan/7769667/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C2=CC=CC=C2)C=C1) `REAL300000086776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086776 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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.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, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [57, 58, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 79, 79, 78, 79, 79, 79, 79, 79, 79, 79, 79, 58, 58, 58, 11, 1, 1, 1, 79, 79, 79, 79, 79, 79, 79, 79, 79] 79 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 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: REAL300000086776 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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.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, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [12, 3, 12, 12, 37, 79, 79, 79, 79, 79, 79, 79, 79, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 37, 79, 79, 79, 3, 3, 1, 1, 1, 1, 1, 3, 3] 79 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: 159 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086776 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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.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, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 29, 79, 79, 79, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 7, 7, 7, 29, 79, 79, 79, 1, 1, 3, 3, 1, 3, 3, 1, 1] 79 rigid atoms, others: [32, 1, 33, 40, 39, 13, 14, 15, 16, 17, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 141 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086776 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086776 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086776/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086776 Building REAL300000086777 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086777' /scratch/stefan/7769667/working/building/REAL300000086777 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086777 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086777/0 /scratch/stefan/7769667/working/building/REAL300000086777 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/809 `/scratch/stefan/7769667/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC2=CC=CC=C2C=C1) `REAL300000086777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086777 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [47, 48, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 100, 100, 100, 100, 100, 100, 100, 100, 100, 48, 48, 48, 12, 1, 1, 1, 100, 100, 100, 100, 100, 100, 100] 100 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086777 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 48, 100, 100, 100, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 48, 100, 100, 100, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [32, 1, 34, 35, 36, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 195 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086777 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086777 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086777/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086777 Building REAL300000086778 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086778' /scratch/stefan/7769667/working/building/REAL300000086778 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086778 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086778/0 /scratch/stefan/7769667/working/building/REAL300000086778 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/810 `/scratch/stefan/7769667/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OC) `REAL300000086778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086778 none CCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [34, 9, 1, 1, 1, 1, 1, 1, 6, 6, 29, 84, 84, 83, 84, 84, 84, 84, 84, 1, 1, 1, 3, 34, 34, 34, 34, 34, 1, 1, 6, 29, 84, 84, 84, 1, 3, 3, 3] 201 rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 19, 20, 21, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086778 none CCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [201, 183, 84, 84, 84, 84, 32, 32, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 148, 201, 201, 201, 201, 201, 84, 84, 32, 7, 1, 1, 1, 84, 148, 148, 148] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 492 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086778 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086778 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086778/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086778 Building REAL300000086779 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086779' /scratch/stefan/7769667/working/building/REAL300000086779 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086779 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086779/0 /scratch/stefan/7769667/working/building/REAL300000086779 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/811 `/scratch/stefan/7769667/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1O) `REAL300000086779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086779 none CCOC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 340 conformations in input total number of sets (complete confs): 340 using faster count positions algorithm for large data unique positions, atoms: [39, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 33, 107, 107, 107, 107, 107, 107, 107, 107, 1, 1, 40, 40, 40, 39, 39, 1, 1, 1, 9, 33, 107, 107, 107, 2] 340 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 21, 27, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 300 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086779 none CCOC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 340 conformations in input total number of sets (complete confs): 340 using faster count positions algorithm for large data unique positions, atoms: [170, 163, 107, 107, 107, 107, 107, 64, 64, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 107, 107, 170, 170, 170, 170, 170, 107, 107, 107, 64, 11, 1, 1, 1, 214] 340 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 521 number of broken/clashed sets: 133 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086779 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086779 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086779/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086779 Building REAL300000086780 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086780' /scratch/stefan/7769667/working/building/REAL300000086780 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086780 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086780/0 /scratch/stefan/7769667/working/building/REAL300000086780 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/812 `/scratch/stefan/7769667/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C2CCCCC2=C1) `REAL300000086780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086780 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C2CCCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [51, 52, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 107, 107, 107, 107, 107, 107, 107, 107, 107, 52, 52, 52, 12, 1, 1, 1, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107] 107 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 1, 2, 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: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086780 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C2CCCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 44, 107, 107, 107, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 44, 107, 107, 107, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 107 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 204 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086780 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086780 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086780/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086780 Building REAL300000086781 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086781' /scratch/stefan/7769667/working/building/REAL300000086781 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086781 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086781/0 /scratch/stefan/7769667/working/building/REAL300000086781 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/813 `/scratch/stefan/7769667/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C2C1=CC(C(C)C)=CC=C2C) `REAL300000086781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086781 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C2C1=CC(C(C)C)=CC=C2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 31, 95, 95, 95, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 5, 31, 95, 95, 95, 1, 2, 3, 3, 3, 2, 2, 2, 1, 1, 2, 2, 2] 95 rigid atoms, others: [0, 1, 2, 3, 4, 44, 45, 16, 17, 18, 19, 20, 23, 24, 25, 26, 30, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086781 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C2C1=CC(C(C)C)=CC=C2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 51, 51, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 51, 13, 1, 1, 1, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95] 95 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086781 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086781 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086781/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086781 Building REAL300000086782 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086782' /scratch/stefan/7769667/working/building/REAL300000086782 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086782 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086782/0 /scratch/stefan/7769667/working/building/REAL300000086782 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/814 `/scratch/stefan/7769667/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CN(CC3=CC=CC=C3)N=C2C2=CC=CC=C2)C=N1) `REAL300000086782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086782 none O=C([O-])C1=CC=C(NN=CC2=CN(CC3=CC=CC=C3)N=C2C2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 60, 60, 31, 9, 9, 5, 5, 5, 5, 5, 21, 40, 40, 28, 40, 40, 5, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 31, 9, 5, 21, 21, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 60] 201 rigid atoms, others: [42, 43, 44, 45, 46, 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, 47]) total number of confs: 274 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086782 none O=C([O-])C1=CC=C(NN=CC2=CN(CC3=CC=CC=C3)N=C2C2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 7, 31, 31, 46, 46, 46, 143, 201, 201, 167, 201, 201, 46, 46, 46, 60, 60, 46, 60, 60, 1, 1, 1, 1, 7, 31, 46, 143, 143, 201, 201, 201, 201, 201, 60, 60, 46, 60, 60, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 47, 28, 29, 30, 31] set([0, 2, 8, 9, 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, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 770 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086782 none O=C([O-])C1=CC=C(NN=CC2=CN(CC3=CC=CC=C3)N=C2C2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 106, 34, 34, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 40, 40, 19, 40, 40, 201, 201, 201, 201, 106, 34, 19, 5, 5, 1, 1, 1, 1, 1, 40, 40, 19, 40, 40, 201] 201 rigid atoms, others: [37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47]) total number of confs: 534 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086782 none O=C([O-])C1=CC=C(NN=CC2=CN(CC3=CC=CC=C3)N=C2C2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 21, 6, 6, 1, 1, 1, 1, 1, 9, 19, 19, 12, 19, 19, 1, 1, 1, 5, 5, 1, 5, 5, 46, 46, 46, 46, 21, 6, 1, 9, 9, 19, 19, 19, 19, 19, 5, 5, 1, 5, 5, 46] 201 rigid atoms, others: [34, 9, 10, 11, 12, 13, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086782 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086782 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086782/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086782 Building REAL300000086783 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086783' /scratch/stefan/7769667/working/building/REAL300000086783 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086783 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086783/0 /scratch/stefan/7769667/working/building/REAL300000086783 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/815 `/scratch/stefan/7769667/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NC2=NC(Cl)=C(C=NNC3=CC=C(C(=O)[O-])N=C3)S2)C=C1) `REAL300000086783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086783 none CC1=CC=C(NC2=NC(Cl)=C(C=NNC3=CC=C(C(=O)[O-])N=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 11, 29, 29, 29, 29, 29, 63, 63, 121, 201, 201, 201, 201, 201, 201, 201, 201, 29, 1, 1, 2, 2, 2, 1, 1, 11, 63, 121, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 24, 25, 29, 30, 37] 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]) total number of confs: 489 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086783 none CC1=CC=C(NC2=NC(Cl)=C(C=NNC3=CC=C(C(=O)[O-])N=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 191, 82, 82, 82, 82, 82, 47, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 201, 201, 201, 201, 191, 47, 11, 1, 1, 1, 201, 201] 201 rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 450 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086783 none CC1=CC=C(NC2=NC(Cl)=C(C=NNC3=CC=C(C(=O)[O-])N=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [28, 16, 28, 28, 12, 1, 1, 1, 1, 1, 1, 1, 9, 9, 35, 82, 82, 82, 82, 82, 82, 82, 82, 1, 28, 28, 28, 28, 28, 28, 28, 12, 9, 35, 82, 82, 82, 28, 28] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 23] set([0, 1, 2, 3, 4, 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]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086783 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086783 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086783/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086783 Building REAL300000086784 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086784' /scratch/stefan/7769667/working/building/REAL300000086784 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086784 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086784/0 /scratch/stefan/7769667/working/building/REAL300000086784 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/816 `/scratch/stefan/7769667/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1Br) `REAL300000086784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086784 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 17, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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, 12, 12, 12, 68, 197, 197, 197, 197, 197, 197, 197, 197, 1, 1, 1, 4, 4, 4, 1, 1, 13, 13, 13, 68, 197, 197, 197, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 19, 20, 21, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 360 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086784 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 17, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 160, 197, 197, 59, 59, 59, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 197, 197, 197, 201, 201, 201, 197, 197, 59, 59, 59, 11, 1, 1, 1, 197] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 449 number of broken/clashed sets: 77 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086784 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086784 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086784/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086784 Building REAL300000086785 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086785' /scratch/stefan/7769667/working/building/REAL300000086785 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086785 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086785/0 /scratch/stefan/7769667/working/building/REAL300000086785 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/817 `/scratch/stefan/7769667/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=NC(Cl)=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(N2CCCC2)=N1) `REAL300000086785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086785 none NC1=NC(Cl)=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(N2CCCC2)=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 8, 5, 5, 5, 5, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 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, 1, 7, 7, 26, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 6, 6, 6, 6, 1, 2, 2, 7, 26, 68, 68, 68, 6, 6, 6, 6, 6, 6, 6, 6] 70 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086785 none NC1=NC(Cl)=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(N2CCCC2)=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 8, 5, 5, 5, 5, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 18, 18, 38, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 38, 70, 70, 70, 1, 1, 1, 1, 1, 1, 1, 1] 70 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086785 none NC1=NC(Cl)=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(N2CCCC2)=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 8, 5, 5, 5, 5, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [68, 56, 68, 68, 68, 46, 46, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68, 70, 70, 70, 70, 68, 68, 68, 46, 11, 1, 1, 1, 70, 70, 70, 70, 70, 70, 70, 70] 70 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086785 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086785 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086785/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086785 Building REAL300000086786 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086786' /scratch/stefan/7769667/working/building/REAL300000086786 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086786 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086786/0 /scratch/stefan/7769667/working/building/REAL300000086786 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/818 `/scratch/stefan/7769667/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1O) `REAL300000086786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086786 none CC[NH+](CC)CC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 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, 7, 6] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7] 1 hydrogens need rotated 210 conformations in input total number of sets (complete confs): 210 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 5, 7, 7, 7, 1, 1, 1, 1, 1, 10, 10, 10, 27, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 1, 11, 11, 11, 27, 43, 43, 43, 1, 1, 2] 210 rigid atoms, others: [6, 39, 8, 9, 10, 7, 47, 48, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 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, 49]) total number of confs: 134 number of broken/clashed sets: 210 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086786 none CC[NH+](CC)CC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 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, 7, 6] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7] 1 hydrogens need rotated 210 conformations in input total number of sets (complete confs): 210 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 77, 105, 105, 105, 43, 43, 43, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 23, 25, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 77, 77, 43, 13, 13, 13, 3, 1, 1, 1, 43, 43, 86] 210 rigid atoms, others: [45, 46, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49]) total number of confs: 545 number of broken/clashed sets: 210 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086786 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086786/1 /scratch/stefan/7769667/working/building/REAL300000086786 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/819 `/scratch/stefan/7769667/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1[O-]) `REAL300000086786.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086786 none CC[NH+](CC)CC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 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, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 12, 12, 12, 19, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 12, 12, 12, 19, 29, 29, 29, 1, 1] 39 rigid atoms, others: [6, 39, 8, 9, 10, 7, 47, 48, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 74 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086786 none CC[NH+](CC)CC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 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, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 29, 29, 29, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 15, 15, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 29, 11, 11, 11, 3, 1, 1, 1, 29, 29] 39 rigid atoms, others: [45, 46, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48]) total number of confs: 137 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086786 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086786 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086786/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086786/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086786 Building REAL300000086787 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086787' /scratch/stefan/7769667/working/building/REAL300000086787 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086787 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086787/0 /scratch/stefan/7769667/working/building/REAL300000086787 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/820 `/scratch/stefan/7769667/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=C(Cl)C=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OC) `REAL300000086787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086787 none CCCOC1=C(Cl)C=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [18, 10, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 66, 66, 66, 66, 66, 66, 66, 66, 1, 1, 1, 4, 23, 23, 23, 22, 22, 10, 10, 1, 6, 22, 66, 66, 66, 1, 4, 4, 4] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 38] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086787 none CCCOC1=C(Cl)C=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [201, 177, 117, 66, 66, 66, 66, 66, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 134, 201, 201, 201, 201, 201, 177, 177, 66, 27, 7, 1, 1, 1, 66, 134, 134, 134] 201 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 788 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086787 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086787 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086787/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086787 Building REAL300000086788 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086788' /scratch/stefan/7769667/working/building/REAL300000086788 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086788 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086788/0 /scratch/stefan/7769667/working/building/REAL300000086788 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/821 `/scratch/stefan/7769667/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(O)C(C[NH+]2CCCCC2)=C1) `REAL300000086788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086788 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(O)C(C[NH+]2CCCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 1, 5, 9, 6, 5, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [15, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 33, 33, 16, 27, 33, 33, 53, 64, 64, 64, 64, 64, 64, 33, 16, 16, 16, 7, 1, 1, 1, 33, 33, 66, 53, 53, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 33] 128 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 318 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086788 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(O)C(C[NH+]2CCCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 1, 5, 9, 6, 5, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 23, 23, 46, 64, 64, 64, 64, 64, 64, 64, 64, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 23, 23, 23, 46, 64, 64, 64, 8, 8, 16, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8] 128 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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, 50]) total number of confs: 179 number of broken/clashed sets: 65 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086788 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(O)C(C[NH+]2CCCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 1, 5, 9, 6, 5, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 23, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 1, 10, 10, 10, 23, 33, 33, 33, 1, 1, 2, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1] 128 rigid atoms, others: [1, 35, 36, 13, 14, 15, 16, 17, 18, 19, 50, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 105 number of broken/clashed sets: 65 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086788 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086788/1 /scratch/stefan/7769667/working/building/REAL300000086788 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/822 `/scratch/stefan/7769667/working/3D/822' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C([O-])C(C[NH+]2CCCCC2)=C1) `REAL300000086788.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086788/1/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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086788 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C([O-])C(C[NH+]2CCCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 1, 5, 9, 6, 5, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [13, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 42, 42, 20, 42, 42, 42, 51, 59, 59, 59, 59, 59, 59, 42, 14, 14, 14, 5, 1, 1, 1, 42, 42, 51, 51, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 42] 59 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 233 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086788 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C([O-])C(C[NH+]2CCCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 1, 5, 9, 6, 5, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 3, 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] 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: [25, 7, 25, 25, 49, 59, 59, 59, 59, 59, 59, 59, 59, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 25, 25, 25, 49, 59, 59, 59, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7] 59 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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, 49]) total number of confs: 162 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086788 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C([O-])C(C[NH+]2CCCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 1, 5, 9, 6, 5, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 3, 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] 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: [11, 1, 11, 11, 30, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 1, 11, 11, 11, 30, 42, 42, 42, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 59 rigid atoms, others: [1, 35, 36, 49, 13, 14, 15, 16, 17, 18, 19, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086788 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086788 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086788/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086788/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086788 Building REAL300000086789 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086789' /scratch/stefan/7769667/working/building/REAL300000086789 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086789 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086789/0 /scratch/stefan/7769667/working/building/REAL300000086789 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/823 `/scratch/stefan/7769667/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C2OCOC2=C1) `REAL300000086789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086789 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C2OCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 12, 5, 12, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 7] 0 hydrogens need rotated 201 conformations 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, 7, 7, 32, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 1, 1, 6, 6, 5, 6, 6, 6, 6, 6, 2, 2, 2, 1, 7, 32, 83, 83, 83, 2, 2, 2, 6, 6, 6, 6, 6] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086789 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C2OCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 12, 5, 12, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 7] 0 hydrogens 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, 6, 6, 6, 28, 28, 96, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 28, 96, 201, 201, 201, 6, 6, 6, 1, 1, 1, 1, 1] 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]) total number of confs: 417 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086789 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C2OCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 12, 5, 12, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 52, 52, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 201, 201, 201, 201, 201, 201, 201, 201, 83, 83, 83, 83, 52, 11, 1, 1, 1, 83, 83, 83, 201, 201, 201, 201, 201] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 305 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086789 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086789/1 /scratch/stefan/7769667/working/building/REAL300000086789 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/824 `/scratch/stefan/7769667/working/3D/824' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C2OCOC2=C1) `REAL300000086789.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086789/1/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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086789 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C2OCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 12, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 27, 28, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 5, 5, 2, 2, 2, 1, 8, 8, 55, 55, 55, 2, 2, 2, 5, 5, 5, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086789 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C2OCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 12, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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, 7] 0 hydrogens 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, 5, 5, 5, 29, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 29, 29, 201, 201, 201, 5, 5, 5, 1, 1, 1, 1, 1] 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086789 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1C1=CC=C2OCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 1, 1, 1, 1, 12, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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, 7] 0 hydrogens 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, 19, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 201, 201, 201, 201, 201, 201, 201, 201, 55, 55, 55, 55, 18, 19, 1, 1, 1, 55, 55, 55, 201, 201, 201, 201, 201] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 308 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086789 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086789 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086789/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086789/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086789 Building REAL300000086790 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086790' /scratch/stefan/7769667/working/building/REAL300000086790 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086790 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086790/0 /scratch/stefan/7769667/working/building/REAL300000086790 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/825 `/scratch/stefan/7769667/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(N3C=CN=C3)C=C2)C=N1) `REAL300000086790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086790 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3C=CN=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 33, 33, 38, 38, 34, 34, 72, 72, 71, 71, 38, 38, 1, 1, 1, 1, 12, 33, 38, 38, 72, 72, 71, 38, 38, 1] 72 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086790 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3C=CN=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 30, 11, 11, 1, 1, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 72, 72, 72, 72, 29, 10, 7, 7, 1, 1, 1, 7, 7, 72] 72 rigid atoms, others: [13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 169 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086790 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3C=CN=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 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: [38, 38, 38, 38, 38, 38, 16, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 38, 38, 38, 38, 16, 6, 1, 1, 7, 6, 7, 1, 1, 38] 72 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086790 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086790 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086790/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086790 Building REAL300000086791 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086791' /scratch/stefan/7769667/working/building/REAL300000086791 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086791 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086791/0 /scratch/stefan/7769667/working/building/REAL300000086791 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/826 `/scratch/stefan/7769667/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C(CCCC2=CC=CC=C2)C2=CC=CC=C2)C=N1) `REAL300000086791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086791 none O=C([O-])C1=CC=C(NN=C(CCCC2=CC=CC=C2)C2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', '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.ar', '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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 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] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 6, 21, 21, 104, 134, 199, 201, 201, 200, 201, 201, 21, 39, 39, 21, 39, 39, 1, 1, 1, 1, 6, 104, 104, 161, 161, 199, 199, 201, 201, 201, 201, 201, 39, 39, 32, 39, 39, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 46, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 1117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086791 none O=C([O-])C1=CC=C(NN=C(CCCC2=CC=CC=C2)C2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', '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.ar', '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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 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] 0 hydrogens 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, 39, 39, 15, 4, 4, 1, 4, 27, 35, 60, 62, 62, 61, 62, 62, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 15, 27, 27, 40, 40, 60, 60, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 39] 201 rigid atoms, others: [43, 9, 42, 23, 44, 45, 19, 20, 21, 22, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 46]) total number of confs: 373 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086791 none O=C([O-])C1=CC=C(NN=C(CCCC2=CC=CC=C2)C2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', '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.ar', '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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 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, 103, 33, 33, 7, 5, 3, 1, 1, 1, 1, 1, 1, 1, 33, 62, 62, 33, 62, 62, 201, 201, 201, 201, 103, 7, 7, 5, 5, 3, 3, 1, 1, 1, 1, 1, 62, 62, 52, 62, 62, 201] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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, 35, 41, 42, 43, 44, 45, 46]) total number of confs: 639 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086791 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086791 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086791/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086791 Building REAL300000086792 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086792' /scratch/stefan/7769667/working/building/REAL300000086792 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086792 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086792/0 /scratch/stefan/7769667/working/building/REAL300000086792 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/827 `/scratch/stefan/7769667/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C12) `REAL300000086792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086792 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 55, 164, 164, 164, 164, 164, 164, 164, 164, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 9, 9, 9, 55, 164, 164, 164, 1, 1, 1, 1] 164 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 19, 20, 21, 22, 23, 24, 38, 28, 29, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 291 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086792 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 164, 66, 66, 66, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 66, 66, 66, 13, 1, 1, 1, 164, 164, 164, 164] 164 rigid atoms, others: [34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 241 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086792 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086792 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086792/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086792 Building REAL300000086793 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086793' /scratch/stefan/7769667/working/building/REAL300000086793 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086793 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086793/0 /scratch/stefan/7769667/working/building/REAL300000086793 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/828 `/scratch/stefan/7769667/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3F)O2)C=N1) `REAL300000086793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086793 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3F)O2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 59, 59, 95, 95, 95, 95, 201, 201, 126, 201, 201, 201, 95, 1, 1, 1, 1, 10, 59, 95, 95, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 562 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086793 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3F)O2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 107, 40, 40, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 107, 40, 13, 13, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 432 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086793 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3F)O2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 95, 95, 34, 7, 7, 1, 1, 1, 1, 1, 1, 13, 13, 1, 13, 13, 13, 1, 95, 95, 95, 95, 34, 7, 1, 1, 13, 13, 10, 13, 95] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086793 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086793 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086793/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086793 Building REAL300000086794 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086794' /scratch/stefan/7769667/working/building/REAL300000086794 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086794 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086794/0 /scratch/stefan/7769667/working/building/REAL300000086794 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/829 `/scratch/stefan/7769667/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1C(C)=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1C) `REAL300000086794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086794 none COCCN1C(C)=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 12, 5, 5, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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, 6, 2, 1, 1, 1, 1, 1, 1, 1, 8, 8, 44, 117, 117, 117, 117, 117, 117, 117, 117, 1, 1, 25, 25, 25, 6, 6, 2, 2, 2, 2, 2, 1, 8, 44, 117, 117, 117, 2, 2, 2] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 9, 21, 22] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086794 none COCCN1C(C)=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 12, 5, 5, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 163, 117, 117, 117, 117, 117, 51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 201, 201, 201, 163, 163, 117, 117, 117, 117, 51, 11, 1, 1, 1, 117, 117, 117] 201 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 647 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086794 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086794/1 /scratch/stefan/7769667/working/building/REAL300000086794 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/830 `/scratch/stefan/7769667/working/3D/830' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1C(C)=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C1C) `REAL300000086794.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086794 none COCCN1C(C)=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 12, 5, 5, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 2, 2, 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: [18, 6, 2, 1, 1, 1, 1, 1, 1, 1, 8, 42, 42, 85, 85, 85, 85, 85, 85, 85, 85, 1, 1, 19, 19, 19, 6, 6, 2, 2, 2, 2, 2, 1, 8, 8, 85, 85, 85, 2, 2, 2] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 9, 21, 22] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086794 none COCCN1C(C)=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 12, 5, 5, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 161, 85, 85, 85, 85, 85, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 85, 85, 201, 201, 201, 201, 201, 161, 161, 85, 85, 85, 85, 26, 27, 1, 1, 1, 85, 85, 85] 201 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 818 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086794 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086794 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086794/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086794/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086794 Building REAL300000086795 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086795' /scratch/stefan/7769667/working/building/REAL300000086795 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086795 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086795/0 /scratch/stefan/7769667/working/building/REAL300000086795 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/831 `/scratch/stefan/7769667/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1[N+](=O)[O-]) `REAL300000086795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086795 none CC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 11, 11, 8, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 34, 74, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 10, 34, 75, 75, 75, 1] 75 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 17, 18, 19, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086795 none CC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 11, 11, 8, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 66, 75, 75, 47, 47, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 47, 12, 1, 1, 1, 75] 75 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086795 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086795 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086795/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086795 Building REAL300000086796 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086796' /scratch/stefan/7769667/working/building/REAL300000086796 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086796 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086796/0 /scratch/stefan/7769667/working/building/REAL300000086796 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/832 `/scratch/stefan/7769667/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC1=CC=CC=C1) `REAL300000086796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086796 none CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 10, 1, 1, 1, 1, 1, 3, 3, 7, 12, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 9, 36, 65, 65, 39, 65, 65, 18, 18, 18, 18, 18, 1, 3, 7, 13, 13, 13, 1, 1, 36, 36, 65, 65, 65, 65, 65] 201 rigid atoms, others: [34, 3, 4, 5, 6, 40, 41, 2, 18, 19, 20, 21] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086796 none CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7] 0 hydrogens 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, 119, 65, 65, 65, 30, 65, 89, 89, 109, 178, 178, 178, 178, 178, 178, 178, 178, 65, 65, 15, 3, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 123, 65, 89, 109, 178, 178, 178, 65, 65, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 22, 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, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 640 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086796 none CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7] 0 hydrogens 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, 54, 13, 13, 13, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 69, 156, 178, 178, 165, 178, 178, 65, 65, 65, 65, 65, 13, 7, 3, 1, 1, 1, 13, 13, 156, 156, 178, 178, 178, 178, 178] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 683 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086796 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086796 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086796/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086796 Building REAL300000086797 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086797' /scratch/stefan/7769667/working/building/REAL300000086797 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086797 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086797/0 /scratch/stefan/7769667/working/building/REAL300000086797 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/833 `/scratch/stefan/7769667/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2CCS(=O)(=O)C3=CC=CC=C32)C=N1) `REAL300000086797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086797 none O=C([O-])C1=CC=C(NN=C2CCS(=O)(=O)C3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 12, 29, 29, 29, 29, 29, 29, 29, 29, 1] 29 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 54 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086797 none O=C([O-])C1=CC=C(NN=C2CCS(=O)(=O)C3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 29] 29 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33] set([0, 1, 2, 3, 4, 5, 6, 34, 21, 22, 23, 24, 25]) total number of confs: 47 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086797 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086797 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086797/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086797 Building REAL300000086798 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086798' /scratch/stefan/7769667/working/building/REAL300000086798 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086798 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086798/0 /scratch/stefan/7769667/working/building/REAL300000086798 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/834 `/scratch/stefan/7769667/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(C(C)(C)C)=C1O) `REAL300000086798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086798 none CC(C)(C)C1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(C(C)(C)C)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 5, 5, 5, 1, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 7, 7] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 10, 10, 30, 60, 60, 60, 60, 60, 60, 60, 60, 1, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 10, 30, 60, 60, 60, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 120 rigid atoms, others: [1, 36, 5, 6, 7, 42, 19, 20, 21, 25, 4, 26] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 137 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086798 none CC(C)(C)C1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(C(C)(C)C)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 5, 5, 5, 1, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 7, 7] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 60, 60, 43, 43, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 50, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 43, 13, 1, 1, 1, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 120] 120 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 257 number of broken/clashed sets: 120 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086798 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086798 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086798/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086798 Building REAL300000086799 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086799' /scratch/stefan/7769667/working/building/REAL300000086799 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086799 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086799/0 /scratch/stefan/7769667/working/building/REAL300000086799 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/835 `/scratch/stefan/7769667/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C([O-])C([N+](=O)[O-])=C2)C=N1) `REAL300000086799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086799 none O=C([O-])C1=CC=C(NN=CC2=CC=C([O-])C([N+](=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 11, 41, 41, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 11, 41, 57, 57, 57, 1] 57 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086799 none O=C([O-])C1=CC=C(NN=CC2=CC=C([O-])C([N+](=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 57, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 57, 57, 57, 57, 27, 9, 1, 1, 1, 57] 57 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086799 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086799 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086799/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086799 Building REAL300000086800 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086800' /scratch/stefan/7769667/working/building/REAL300000086800 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086800 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086800/0 /scratch/stefan/7769667/working/building/REAL300000086800 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/836 `/scratch/stefan/7769667/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C2=C(C=CC=C2)C2=C1C=CC(C=NNC1=CC=C(C(=O)[O-])N=C1)=C2) `REAL300000086800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086800 none CCN1C2=C(C=CC=C2)C2=C1C=CC(C=NNC1=CC=C(C(=O)[O-])N=C1)=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 46, 131, 131, 130, 130, 131, 131, 131, 131, 1, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 10, 46, 131, 131, 131, 1] 167 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 32, 33, 34, 35, 36, 37, 43] set([0, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086800 none CCN1C2=C(C=CC=C2)C2=C1C=CC(C=NNC1=CC=C(C(=O)[O-])N=C1)=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 65, 65, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 131, 167, 167, 167, 167, 167, 131, 131, 131, 131, 131, 131, 65, 13, 1, 1, 1, 131] 167 rigid atoms, others: [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, 38, 39, 43]) total number of confs: 413 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086800 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086800 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086800/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086800 Building REAL300000086801 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086801' /scratch/stefan/7769667/working/building/REAL300000086801 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086801 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086801/0 /scratch/stefan/7769667/working/building/REAL300000086801 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/837 `/scratch/stefan/7769667/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CCC(C)N=NC2=CC=C(C(=O)[O-])N=C2)C=C1) `REAL300000086801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086801 none COC1=CC=C(CCC(C)N=NC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 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, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 7, 11, 40, 41, 133, 133, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 7, 7, 11, 11, 41, 40, 41, 41, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 21, 22, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 430 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086801 none COC1=CC=C(CCC(C)N=NC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 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, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 130, 201, 201, 130, 105, 46, 9, 46, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 126, 130, 111, 111, 46, 46, 46, 46, 1, 1, 1, 201, 201] 201 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 936 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086801 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086801 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086801/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086801 Building REAL300000086802 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086802' /scratch/stefan/7769667/working/building/REAL300000086802 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086802 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086802/0 /scratch/stefan/7769667/working/building/REAL300000086802 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/838 `/scratch/stefan/7769667/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(N2CCCCC2)C=C1) `REAL300000086802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086802 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(N2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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, 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: [55, 56, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 100, 100, 68, 85, 117, 117, 117, 117, 117, 100, 100, 56, 56, 56, 11, 1, 1, 1, 100, 100, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 100, 100] 117 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 326 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: REAL300000086802 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(N2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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, 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: [22, 1, 22, 22, 63, 117, 117, 117, 117, 117, 117, 117, 117, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 60, 117, 117, 117, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 117 rigid atoms, others: [34, 35, 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, 44, 45]) total number of confs: 266 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086802 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(N2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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, 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: [7, 1, 7, 7, 32, 100, 100, 100, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 7, 7, 7, 32, 100, 100, 100, 1, 1, 10, 10, 10, 11, 10, 10, 10, 11, 10, 10, 1, 1] 117 rigid atoms, others: [32, 1, 45, 33, 44, 13, 14, 15, 16, 17, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086802 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086802 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086802/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086802 Building REAL300000086803 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086803' /scratch/stefan/7769667/working/building/REAL300000086803 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086803 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086803/0 /scratch/stefan/7769667/working/building/REAL300000086803 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/839 `/scratch/stefan/7769667/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C=C1Cl) `REAL300000086803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086803 none CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [97, 51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 108, 108, 65, 108, 108, 108, 108, 97, 97, 97, 97, 97, 11, 1, 1, 1, 108, 108, 108] 112 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30] set([0, 1, 2, 3, 33, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 597 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086803 none CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [24, 9, 1, 9, 9, 41, 108, 108, 108, 108, 108, 108, 108, 108, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 41, 108, 108, 108, 1, 1, 1] 112 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 262 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086803 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086803 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086803/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086803 Building REAL300000086804 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086804' /scratch/stefan/7769667/working/building/REAL300000086804 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086804 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086804/0 /scratch/stefan/7769667/working/building/REAL300000086804 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/840 `/scratch/stefan/7769667/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C=NNC3=CC=C(C(=O)[O-])N=C3)=CC2=CC=C1) `REAL300000086804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086804 none COC1=C2OC(C=NNC3=CC=C(C(=O)[O-])N=C3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 41, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 3, 3, 3, 7, 41, 105, 105, 105, 1, 1, 1, 1] 105 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 18, 19, 20, 21, 22, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086804 none COC1=C2OC(C=NNC3=CC=C(C(=O)[O-])N=C3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 105, 67, 67, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 105, 105, 105, 67, 13, 1, 1, 1, 105, 105, 105, 105] 105 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 158 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086804 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086804 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086804/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086804 Building REAL300000086805 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086805' /scratch/stefan/7769667/working/building/REAL300000086805 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086805 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086805/0 /scratch/stefan/7769667/working/building/REAL300000086805 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/841 `/scratch/stefan/7769667/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(CC(C)C)C=C1) `REAL300000086805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086805 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [62, 63, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 126, 126, 64, 69, 191, 191, 200, 126, 126, 63, 63, 63, 11, 1, 1, 1, 126, 126, 191, 191, 200, 200, 200, 200, 200, 200, 200, 126, 126] 200 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 1, 2, 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, 41, 42]) total number of confs: 986 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086805 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 33, 126, 126, 126, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 4, 5, 7, 1, 1, 6, 6, 6, 33, 126, 126, 126, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 1, 1] 200 rigid atoms, others: [1, 41, 42, 13, 14, 15, 16, 17, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 238 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086805 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086805 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086805/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086805 Building REAL300000086806 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086806' /scratch/stefan/7769667/working/building/REAL300000086806 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086806 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086806/0 /scratch/stefan/7769667/working/building/REAL300000086806 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/842 `/scratch/stefan/7769667/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1[N+](=O)[O-]) `REAL300000086806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086806 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 33, 33, 33, 33, 33, 33, 33, 33, 29, 29, 29, 11, 1, 1, 1, 33, 33, 33, 33] 33 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28] set([0, 1, 2, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086806 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 13, 33, 33, 33, 1, 1, 1, 1] 33 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086806 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086806 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086806/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086806 Building REAL300000086807 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086807' /scratch/stefan/7769667/working/building/REAL300000086807 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086807 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086807/0 /scratch/stefan/7769667/working/building/REAL300000086807 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/843 `/scratch/stefan/7769667/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1[N+](=O)[O-]) `REAL300000086807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086807 none CC(C)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 8, 11, 11, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 35, 75, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 11, 35, 76, 76, 76, 1] 76 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 19, 20, 21, 38, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086807 none CC(C)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 8, 11, 11, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 67, 76, 76, 48, 48, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 48, 12, 1, 1, 1, 76] 76 rigid atoms, others: [35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 156 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086807 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086807 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086807/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086807 Building REAL300000086808 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086808' /scratch/stefan/7769667/working/building/REAL300000086808 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086808 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086808/0 /scratch/stefan/7769667/working/building/REAL300000086808 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/844 `/scratch/stefan/7769667/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC2=CC=C(OC)C=C2C=C1) `REAL300000086808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086808 none CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC2=CC=C(OC)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 37, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 183, 183, 183, 183, 183, 183, 185, 183, 183, 183, 183, 61, 61, 61, 61, 61, 11, 1, 1, 1, 183, 183, 183, 185, 185, 185, 183, 183, 183] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 379 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086808 none CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC2=CC=C(OC)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 12, 1, 12, 12, 71, 183, 183, 182, 182, 183, 183, 183, 183, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 32, 32, 32, 31, 31, 71, 183, 183, 183, 1, 1, 1, 3, 3, 3, 1, 1, 1] 201 rigid atoms, others: [2, 35, 36, 37, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 464 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086808 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086808 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086808/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086808 Building REAL300000086809 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086809' /scratch/stefan/7769667/working/building/REAL300000086809 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086809 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086809/0 /scratch/stefan/7769667/working/building/REAL300000086809 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/845 `/scratch/stefan/7769667/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Br)=C3OCOC3=C2)C=N1) `REAL300000086809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086809 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=C3OCOC3=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 12, 5, 12, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 36, 36, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 12, 36, 71, 71, 71, 71, 1] 71 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086809 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=C3OCOC3=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 12, 5, 12, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 71, 32, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 32, 11, 1, 1, 1, 1, 71] 71 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 30]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086809 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086809 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086809/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086809 Building REAL300000086810 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086810' /scratch/stefan/7769667/working/building/REAL300000086810 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086810 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086810/0 /scratch/stefan/7769667/working/building/REAL300000086810 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/846 `/scratch/stefan/7769667/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2=CC=CC=C2)C(C)=C1C=NNC1=CC=C(C(=O)[O-])N=C1) `REAL300000086810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086810 none CC1=NN(CC2=CC=CC=C2)C(C)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 11, 12, 9, 12, 11, 1, 1, 1, 1, 10, 10, 46, 95, 95, 95, 95, 95, 95, 95, 95, 2, 2, 2, 7, 7, 11, 12, 11, 12, 11, 2, 2, 2, 10, 46, 95, 95, 95] 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]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086810 none CC1=NN(CC2=CC=CC=C2)C(C)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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: [95, 95, 95, 95, 95, 201, 201, 201, 201, 201, 201, 95, 95, 38, 38, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 201, 201, 201, 201, 201, 201, 201, 95, 95, 95, 38, 11, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 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, 38, 39, 40]) total number of confs: 615 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086810 none CC1=NN(CC2=CC=CC=C2)C(C)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 56, 56, 115, 201, 201, 201, 201, 201, 201, 201, 201, 12, 12, 12, 3, 3, 1, 1, 1, 1, 1, 12, 12, 12, 56, 115, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 473 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086810 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086810 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086810/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086810 Building REAL300000086811 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086811' /scratch/stefan/7769667/working/building/REAL300000086811 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086811 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086811/0 /scratch/stefan/7769667/working/building/REAL300000086811 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/847 `/scratch/stefan/7769667/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2=CC=CC=C2Cl)C(C)=C1C=NNC1=CC=C(C(=O)[O-])N=C1) `REAL300000086811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086811 none CC1=NN(CC2=CC=CC=C2Cl)C(C)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'Cl', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 9, 9, 24, 53, 53, 53, 53, 53, 52, 53, 53, 2, 2, 2, 6, 6, 15, 15, 15, 15, 2, 2, 2, 9, 23, 53, 53, 53] 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086811 none CC1=NN(CC2=CC=CC=C2Cl)C(C)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'Cl', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 123, 201, 201, 201, 201, 201, 201, 53, 53, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 123, 123, 201, 201, 201, 201, 53, 53, 53, 23, 9, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 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, 37, 38, 39, 40]) total number of confs: 513 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086811 none CC1=NN(CC2=CC=CC=C2Cl)C(C)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'Cl', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 67, 67, 105, 201, 201, 201, 201, 201, 201, 201, 201, 15, 15, 15, 6, 6, 1, 1, 1, 1, 15, 15, 15, 67, 105, 201, 201, 201] 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: 471 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086811 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086811 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086811/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086811 Building REAL300000086812 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086812' /scratch/stefan/7769667/working/building/REAL300000086812 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086812 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086812/0 /scratch/stefan/7769667/working/building/REAL300000086812 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/848 `/scratch/stefan/7769667/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC(C)C) `REAL300000086812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086812 none CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 7, 7, 13, 21, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 9, 32, 39, 51, 22, 22, 22, 22, 22, 1, 7, 13, 22, 22, 22, 1, 1, 32, 32, 51, 51, 51, 51, 51, 51, 51] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 19, 20, 21, 38, 37, 31] set([0, 1, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 402 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086812 none CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7] 0 hydrogens 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, 81, 22, 22, 22, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 93, 167, 171, 185, 109, 109, 109, 109, 109, 22, 7, 3, 1, 1, 1, 22, 22, 167, 167, 185, 185, 185, 185, 185, 185, 185] 201 rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 896 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086812 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086812 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086812/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086812 Building REAL300000086813 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086813' /scratch/stefan/7769667/working/building/REAL300000086813 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086813 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086813/0 /scratch/stefan/7769667/working/building/REAL300000086813 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/849 `/scratch/stefan/7769667/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1) `REAL300000086813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086813 none CNS(=O)(=O)C1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 12, 12, 12, 78, 199, 199, 199, 199, 199, 199, 199, 199, 1, 1, 7, 7, 7, 7, 1, 1, 13, 13, 13, 78, 199, 199, 199, 1, 1] 199 rigid atoms, others: [2, 5, 6, 7, 8, 9, 22, 23, 38, 28, 29, 37] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 385 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086813 none CNS(=O)(=O)C1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 76, 199, 199, 73, 199, 199, 67, 67, 67, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 199, 199, 199, 199, 67, 67, 67, 12, 1, 1, 1, 199, 199] 199 rigid atoms, others: [34, 35, 36, 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, 33, 37, 38]) total number of confs: 1012 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086813 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086813 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086813/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086813 Building REAL300000086814 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086814' /scratch/stefan/7769667/working/building/REAL300000086814 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086814 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086814/0 /scratch/stefan/7769667/working/building/REAL300000086814 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/850 `/scratch/stefan/7769667/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC1=C(N=NC2=CC=C(C(=O)[O-])N=C2)CCC1C) `REAL300000086814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086814 none CCCCCC1=C(N=NC2=CC=C(C(=O)[O-])N=C2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 13, 8, 1, 1, 1, 1, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 39, 41, 41, 41, 41, 24, 24, 14, 14, 8, 8, 43, 43, 43, 1, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [4, 5, 6, 7, 40, 39, 18, 19, 20, 21, 36, 38, 37] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43]) total number of confs: 277 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086814 none CCCCCC1=C(N=NC2=CC=C(C(=O)[O-])N=C2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 181, 142, 114, 43, 43, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 201, 201, 201, 201, 201, 181, 180, 144, 144, 114, 114, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43] 201 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 853 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086814 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086814 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086814/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086814 Building REAL300000086815 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086815' /scratch/stefan/7769667/working/building/REAL300000086815 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086815 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086815/0 /scratch/stefan/7769667/working/building/REAL300000086815 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/851 `/scratch/stefan/7769667/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])N=C1)C(C1=CC=CC=C1)C1=CC=CC=C1) `REAL300000086815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086815 none CC(N=NC1=CC=C(C(=O)[O-])N=C1)C(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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.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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 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: [33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 58, 66, 66, 58, 66, 66, 58, 66, 66, 66, 66, 66, 33, 33, 33, 33, 1, 1, 1, 58, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66] 66 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 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, 43]) total number of confs: 309 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: REAL300000086815 none CC(N=NC1=CC=C(C(=O)[O-])N=C1)C(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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.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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 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: [7, 3, 7, 31, 31, 66, 66, 66, 66, 66, 66, 66, 66, 1, 3, 4, 4, 3, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 66, 66, 66, 3, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1] 66 rigid atoms, others: [39, 40, 41, 42, 43, 13, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 125 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086815 none CC(N=NC1=CC=C(C(=O)[O-])N=C1)C(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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.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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 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: [7, 3, 7, 34, 34, 66, 66, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 7, 7, 7, 7, 66, 66, 66, 3, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4] 66 rigid atoms, others: [34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43]) total number of confs: 119 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086815 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086815 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086815/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086815 Building REAL300000086816 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086816' /scratch/stefan/7769667/working/building/REAL300000086816 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086816 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086816/0 /scratch/stefan/7769667/working/building/REAL300000086816 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/852 `/scratch/stefan/7769667/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(C)=O) `REAL300000086816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086816 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 1, 5, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 23, 67, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 7, 27, 27, 4, 4, 4, 1, 7, 23, 68, 68, 68, 1, 1, 27, 27, 27] 201 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 17, 18, 19, 20, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086816 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 1, 5, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 68, 68, 68, 30, 30, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 143, 201, 201, 127, 127, 127, 68, 30, 7, 1, 1, 1, 68, 68, 201, 201, 201] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 570 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086816 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086816 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086816/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086816 Building REAL300000086817 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086817' /scratch/stefan/7769667/working/building/REAL300000086817 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086817 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086817/0 /scratch/stefan/7769667/working/building/REAL300000086817 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/853 `/scratch/stefan/7769667/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC(F)=C(Cl)C=C1Cl) `REAL300000086817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086817 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC(F)=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 15, 1, 16, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [51, 52, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 82, 82, 82, 82, 82, 82, 82, 82, 52, 52, 52, 11, 1, 1, 1, 82, 82] 82 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086817 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC(F)=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 15, 1, 16, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 30, 82, 82, 82, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 30, 82, 82, 82, 1, 1] 82 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 157 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086817 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086817 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086817/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086817 Building REAL300000086818 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086818' /scratch/stefan/7769667/working/building/REAL300000086818 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086818 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086818/0 /scratch/stefan/7769667/working/building/REAL300000086818 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/854 `/scratch/stefan/7769667/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC=C2F)C=N1) `REAL300000086818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086818 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC=C2F)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 15, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 10, 34, 34, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 10, 34, 44, 44, 44, 1] 45 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086818 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC=C2F)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 15, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 45, 44, 44, 44, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 27, 7, 1, 1, 1, 44] 45 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086818 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086818 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086818/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086818 Building REAL300000086819 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086819' /scratch/stefan/7769667/working/building/REAL300000086819 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086819 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086819/0 /scratch/stefan/7769667/working/building/REAL300000086819 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/855 `/scratch/stefan/7769667/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C([N+](=O)[O-])C=C1OC) `REAL300000086819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086819 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C([N+](=O)[O-])C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 8, 11, 11, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 3, 3, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 7, 7, 42, 143, 143, 143, 143, 143, 143, 143, 143, 1, 1, 2, 2, 1, 1, 1, 4, 3, 3, 3, 1, 7, 42, 143, 143, 143, 1, 4, 4, 4] 184 rigid atoms, others: [1, 2, 3, 4, 5, 34, 17, 18, 21, 22, 23, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086819 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C([N+](=O)[O-])C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 8, 11, 11, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [184, 143, 143, 143, 76, 76, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 143, 143, 143, 184, 184, 184, 184, 143, 76, 13, 1, 1, 1, 143, 184, 184, 184] 184 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 376 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086819 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086819 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086819/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086819 Building REAL300000086820 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086820' /scratch/stefan/7769667/working/building/REAL300000086820 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086820 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086820/0 /scratch/stefan/7769667/working/building/REAL300000086820 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/856 `/scratch/stefan/7769667/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OC) `REAL300000086820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086820 none COC1=CC(Br)=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 61, 145, 145, 145, 145, 145, 145, 145, 145, 1, 1, 1, 4, 4, 4, 4, 1, 10, 61, 145, 145, 145, 1, 4, 4, 4] 176 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086820 none COC1=CC(Br)=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [176, 145, 145, 145, 145, 145, 68, 68, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 176, 176, 176, 176, 145, 68, 12, 1, 1, 1, 145, 176, 176, 176] 176 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086820 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086820 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086820/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086820 Building REAL300000086821 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086821' /scratch/stefan/7769667/working/building/REAL300000086821 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086821 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086821/0 /scratch/stefan/7769667/working/building/REAL300000086821 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/857 `/scratch/stefan/7769667/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Br)C=C1) `REAL300000086821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086821 none CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [79, 47, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 76, 76, 76, 76, 76, 76, 79, 79, 79, 79, 79, 11, 1, 1, 1, 76, 76, 76, 76] 97 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 33, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 301 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086821 none CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 1, 7, 7, 24, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 24, 76, 76, 76, 1, 1, 1, 1] 97 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 185 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086821 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086821 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086821/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086821 Building REAL300000086822 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086822' /scratch/stefan/7769667/working/building/REAL300000086822 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086822 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086822/0 /scratch/stefan/7769667/working/building/REAL300000086822 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/858 `/scratch/stefan/7769667/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C=C2F)C=N1) `REAL300000086822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086822 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C=C2F)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 15, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 10, 34, 34, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 10, 34, 42, 42, 42, 1] 43 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086822 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C=C2F)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 15, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 42, 43, 42, 42, 42, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 29, 6, 1, 1, 1, 42] 43 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086822 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086822 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086822/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086822 Building REAL300000086823 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086823' /scratch/stefan/7769667/working/building/REAL300000086823 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086823 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086823/0 /scratch/stefan/7769667/working/building/REAL300000086823 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/859 `/scratch/stefan/7769667/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(Br)=C1) `REAL300000086823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086823 none CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 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: [99, 55, 56, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 161, 161, 149, 161, 161, 161, 99, 99, 99, 99, 99, 11, 1, 1, 1, 161, 161, 160, 161] 191 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 33, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 502 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086823 none CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 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: [39, 13, 1, 13, 13, 63, 161, 161, 161, 161, 161, 161, 161, 161, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 63, 161, 161, 161, 1, 1, 1, 1] 191 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 416 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086823 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086823 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086823/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086823 Building REAL300000086824 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086824' /scratch/stefan/7769667/working/building/REAL300000086824 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086824 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086824/0 /scratch/stefan/7769667/working/building/REAL300000086824 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/860 `/scratch/stefan/7769667/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(O)C(C(C)(C)C)=C1) `REAL300000086824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086824 none CC(C)(C)C1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(O)C(C(C)(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 224 conformations in input total number of sets (complete confs): 224 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 9, 9, 32, 112, 112, 111, 111, 112, 112, 112, 112, 1, 1, 1, 1, 2, 2, 2, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 9, 32, 112, 112, 112, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 224 rigid atoms, others: [1, 4, 5, 6, 7, 19, 20, 21, 22, 36, 26, 52] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 204 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086824 none CC(C)(C)C1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(O)C(C(C)(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 224 conformations in input total number of sets (complete confs): 224 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 112, 112, 112, 70, 70, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 112, 112, 112, 112, 112, 112, 112, 74, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 70, 13, 1, 1, 1, 224, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112] 224 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 568 number of broken/clashed sets: 158 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086824 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086824 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086824/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086824 Building REAL300000086825 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086825' /scratch/stefan/7769667/working/building/REAL300000086825 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086825 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086825/0 /scratch/stefan/7769667/working/building/REAL300000086825 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/861 `/scratch/stefan/7769667/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC([N+](=O)[O-])=C1[O-]) `REAL300000086825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086825 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC([N+](=O)[O-])=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 3, 7, 3, 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, 11, 11, 47, 119, 119, 118, 118, 119, 119, 119, 119, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 1, 11, 47, 119, 119, 119, 1] 119 rigid atoms, others: [1, 2, 3, 4, 5, 33, 17, 18, 19, 22, 23, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086825 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC([N+](=O)[O-])=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 61, 61, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 61, 13, 1, 1, 1, 119] 119 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086825 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086825/1 /scratch/stefan/7769667/working/building/REAL300000086825 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/862 `/scratch/stefan/7769667/working/3D/862' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC([N+](=O)[O-])=C1O) `REAL300000086825.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086825 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC([N+](=O)[O-])=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 11, 11, 60, 134, 134, 134, 134, 134, 134, 134, 134, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 11, 60, 134, 134, 134, 1, 2] 268 rigid atoms, others: [1, 2, 3, 4, 5, 33, 17, 18, 19, 20, 21, 22, 23, 27] set([0, 32, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086825 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC([N+](=O)[O-])=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 134, 134, 68, 68, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 134, 134, 134, 134, 134, 134, 134, 134, 134, 134, 134, 68, 13, 1, 1, 1, 134, 268] 268 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 463 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086825 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086825 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086825/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086825/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086825 Building REAL300000086826 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086826' /scratch/stefan/7769667/working/building/REAL300000086826 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086826 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086826/0 /scratch/stefan/7769667/working/building/REAL300000086826 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/863 `/scratch/stefan/7769667/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=C(C=C1C=NNC1=CC=C(C(=O)[O-])N=C1)OC(C)C2) `REAL300000086826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086826 none COC1=CC2=C(C=C1C=NNC1=CC=C(C(=O)[O-])N=C1)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 55, 126, 126, 125, 125, 126, 126, 126, 126, 1, 1, 1, 1, 4, 4, 4, 1, 1, 12, 55, 126, 126, 126, 1, 2, 2, 2, 1, 1] 126 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 38, 39, 34, 20, 21, 22, 23, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086826 none COC1=CC2=C(C=C1C=NNC1=CC=C(C(=O)[O-])N=C1)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 126, 126, 126, 126, 69, 69, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 126, 126, 126, 126, 126, 69, 13, 1, 1, 1, 126, 126, 126, 126, 126, 126] 126 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 187 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086826 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086826 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086826/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086826 Building REAL300000086827 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086827' /scratch/stefan/7769667/working/building/REAL300000086827 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086827 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086827/0 /scratch/stefan/7769667/working/building/REAL300000086827 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/864 `/scratch/stefan/7769667/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=C(Cl)C=C2)C=N1) `REAL300000086827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086827 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=C(Cl)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 13, 77, 77, 173, 173, 173, 173, 173, 182, 182, 182, 182, 182, 182, 1, 1, 1, 1, 13, 77, 173, 173, 182, 182, 182, 182, 1] 182 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086827 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=C(Cl)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 182, 182, 182, 85, 25, 25, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 182, 182, 182, 182, 85, 25, 6, 6, 1, 1, 1, 1, 182] 182 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 373 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086827 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=C(Cl)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 173, 173, 173, 61, 11, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 173, 173, 173, 173, 61, 11, 1, 1, 6, 6, 6, 6, 173] 182 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 316 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086827 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086827 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086827/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086827 Building REAL300000086828 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086828' /scratch/stefan/7769667/working/building/REAL300000086828 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086828 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086828/0 /scratch/stefan/7769667/working/building/REAL300000086828 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/865 `/scratch/stefan/7769667/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(N3C=NC=N3)C=C2)C=N1) `REAL300000086828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086828 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3C=NC=N3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 10, 26, 26, 31, 31, 26, 26, 59, 59, 60, 59, 31, 31, 1, 1, 1, 1, 10, 26, 31, 31, 59, 60, 31, 31, 1] 60 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32]) 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: REAL300000086828 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3C=NC=N3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 60, 60, 22, 10, 10, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 59, 60, 60, 60, 22, 10, 2, 2, 1, 1, 2, 2, 59] 60 rigid atoms, others: [13, 14, 15, 16, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 123 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086828 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3C=NC=N3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 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: [31, 31, 31, 31, 31, 31, 12, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 31, 31, 31, 31, 12, 6, 1, 1, 2, 2, 1, 1, 31] 60 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 19, 20, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 33]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086828 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086828 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086828/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086828 Building REAL300000086829 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086829' /scratch/stefan/7769667/working/building/REAL300000086829 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086829 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086829/0 /scratch/stefan/7769667/working/building/REAL300000086829 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/866 `/scratch/stefan/7769667/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3)S2)C=N1) `REAL300000086829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086829 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3)S2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 56, 56, 79, 79, 79, 79, 127, 127, 79, 127, 127, 79, 1, 1, 1, 1, 12, 56, 80, 80, 127, 127, 126, 127, 127, 1] 127 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 462 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086829 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3)S2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 127, 127, 88, 37, 37, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 127, 127, 127, 127, 88, 37, 7, 7, 1, 1, 1, 1, 1, 127] 127 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 294 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086829 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3)S2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 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: [80, 80, 80, 80, 80, 80, 41, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 80, 80, 80, 79, 40, 8, 1, 1, 7, 7, 2, 7, 7, 80] 127 rigid atoms, others: [9, 10, 11, 12, 13, 14, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 180 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086829 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086829 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086829/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086829 Building REAL300000086830 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086830' /scratch/stefan/7769667/working/building/REAL300000086830 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086830 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086830/0 /scratch/stefan/7769667/working/building/REAL300000086830 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/867 `/scratch/stefan/7769667/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC1=C(C)ON=C1C) `REAL300000086830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086830 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC1=C(C)ON=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', '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, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 5, 12, 8, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 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, 9, 14, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 9, 28, 72, 72, 72, 72, 72, 72, 4, 4, 4, 1, 5, 9, 15, 15, 15, 1, 1, 28, 28, 72, 72, 72, 72, 72, 72] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 38, 39, 17, 18, 19, 20] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086830 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC1=C(C)ON=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', '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, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 5, 12, 8, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 72, 72, 72, 54, 72, 104, 104, 120, 201, 201, 201, 201, 201, 201, 201, 201, 72, 72, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 72, 104, 120, 201, 201, 201, 72, 72, 8, 8, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [21, 22, 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, 19, 20, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 562 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086830 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC1=C(C)ON=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', '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, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 5, 12, 8, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 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, 15, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 43, 79, 201, 201, 201, 201, 201, 201, 27, 27, 27, 15, 7, 3, 1, 1, 1, 15, 15, 79, 79, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 452 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086830 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086830 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086830/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086830 Building REAL300000086831 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086831' /scratch/stefan/7769667/working/building/REAL300000086831 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086831 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086831/0 /scratch/stefan/7769667/working/building/REAL300000086831 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/868 `/scratch/stefan/7769667/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=NN(C3=CC=CC=C3)N=C2)C=N1) `REAL300000086831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086831 none O=C([O-])C1=CC=C(NN=CC2=NN(C3=CC=CC=C3)N=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 47, 47, 52, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 12, 47, 53, 53, 53, 53, 53, 53, 1] 53 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32]) 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: REAL300000086831 none O=C([O-])C1=CC=C(NN=CC2=NN(C3=CC=CC=C3)N=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 26, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 53, 53, 53, 53, 26, 9, 1, 1, 1, 1, 1, 2, 53] 53 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33]) total number of confs: 103 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086831 none O=C([O-])C1=CC=C(NN=CC2=NN(C3=CC=CC=C3)N=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 26, 8, 8, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 53, 53, 53, 53, 26, 8, 2, 2, 2, 2, 2, 1, 53] 53 rigid atoms, others: [32, 9, 10, 11, 12, 13, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086831 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086831 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086831/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086831 Building REAL300000086832 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086832' /scratch/stefan/7769667/working/building/REAL300000086832 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086832 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086832/0 /scratch/stefan/7769667/working/building/REAL300000086832 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/869 `/scratch/stefan/7769667/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(S(C)(=O)=O)C=C1) `REAL300000086832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086832 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(S(C)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [42, 43, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 55, 55, 44, 44, 95, 95, 95, 55, 55, 43, 43, 43, 11, 1, 1, 1, 55, 55, 95, 95, 95, 55, 55] 95 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 378 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086832 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(S(C)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 20, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 6, 6, 6, 20, 55, 55, 55, 1, 1, 3, 3, 3, 1, 1] 95 rigid atoms, others: [1, 35, 36, 13, 14, 15, 16, 17, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 112 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086832 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086832 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086832/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086832 Building REAL300000086833 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086833' /scratch/stefan/7769667/working/building/REAL300000086833 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086833 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086833/0 /scratch/stefan/7769667/working/building/REAL300000086833 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/870 `/scratch/stefan/7769667/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OCC) `REAL300000086833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086833 none C#CCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [42, 42, 9, 1, 1, 1, 1, 1, 1, 6, 6, 13, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 9, 26, 42, 42, 42, 1, 1, 6, 13, 27, 27, 27, 1, 26, 26, 26, 26, 26] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 35, 20, 21, 22, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086833 none C#CCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [187, 187, 99, 27, 27, 27, 27, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 88, 114, 187, 187, 187, 27, 27, 9, 5, 1, 1, 1, 27, 114, 114, 114, 114, 114] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 755 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086833 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086833 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086833/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086833 Building REAL300000086834 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086834' /scratch/stefan/7769667/working/building/REAL300000086834 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086834 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086834/0 /scratch/stefan/7769667/working/building/REAL300000086834 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/871 `/scratch/stefan/7769667/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21) `REAL300000086834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086834 none C=CCN1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 1, 1, 1, 1, 1, 1, 1, 7, 39, 39, 38, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 18, 18, 18, 7, 7, 7, 39, 39, 39, 1, 1, 1, 1] 74 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 34, 18, 19, 20, 21, 22, 23, 36, 35] set([0, 1, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086834 none C=CCN1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 39, 39, 38, 39, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 74, 74, 74, 74, 74, 11, 1, 1, 1, 39, 39, 39, 39] 74 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086834 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086834 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086834/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086834 Building REAL300000086835 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086835' /scratch/stefan/7769667/working/building/REAL300000086835 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086835 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086835/0 /scratch/stefan/7769667/working/building/REAL300000086835 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/872 `/scratch/stefan/7769667/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC(Br)=CC=C1O) `REAL300000086835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086835 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC(Br)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 85, 85, 85, 85, 85, 85, 85, 54, 54, 54, 11, 1, 1, 1, 85, 85, 85, 170] 170 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 304 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086835 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC(Br)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 36, 85, 85, 85, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 36, 85, 85, 85, 1, 1, 1, 2] 170 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 178 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086835 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086835 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086835/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086835 Building REAL300000086836 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086836' /scratch/stefan/7769667/working/building/REAL300000086836 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086836 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086836/0 /scratch/stefan/7769667/working/building/REAL300000086836 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/873 `/scratch/stefan/7769667/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1N1C(C)=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1C) `REAL300000086836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086836 none COC1=CC=CC=C1N1C(C)=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 6, 6, 6, 34, 34, 117, 201, 201, 201, 201, 201, 201, 201, 201, 6, 7, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 6, 34, 117, 201, 201, 201, 7, 7, 7] 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, 44, 45]) total number of confs: 434 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086836 none COC1=CC=CC=C1N1C(C)=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 103, 103, 103, 103, 103, 47, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 103, 201, 201, 201, 201, 201, 201, 201, 103, 103, 103, 103, 47, 11, 1, 1, 1, 103, 103, 103] 201 rigid atoms, others: [40, 41, 42, 15, 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, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45]) total number of confs: 305 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086836 none COC1=CC=CC=C1N1C(C)=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 6, 6, 2, 6, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 43, 103, 103, 103, 103, 103, 103, 103, 103, 1, 1, 11, 11, 11, 7, 6, 7, 7, 2, 2, 2, 1, 8, 43, 103, 103, 103, 2, 2, 2] 201 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086836 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086836/1 /scratch/stefan/7769667/working/building/REAL300000086836 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/874 `/scratch/stefan/7769667/working/3D/874' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1N1C(C)=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C1C) `REAL300000086836.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086836/1/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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086836 none COC1=CC=CC=C1N1C(C)=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 5, 5, 5, 5, 5, 29, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 5, 29, 29, 201, 201, 201, 5, 5, 5] 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, 44, 45]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086836 none COC1=CC=CC=C1N1C(C)=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 60, 60, 60, 60, 60, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 201, 201, 201, 201, 201, 201, 201, 60, 60, 60, 60, 16, 17, 1, 1, 1, 60, 60, 60] 201 rigid atoms, others: [40, 41, 42, 15, 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, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45]) total number of confs: 297 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086836 none COC1=CC=CC=C1N1C(C)=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 3, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 30, 31, 60, 60, 60, 60, 60, 60, 60, 60, 1, 1, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 8, 8, 60, 60, 60, 2, 2, 2] 201 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086836 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086836 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086836/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086836/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086836 Building REAL300000086837 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086837' /scratch/stefan/7769667/working/building/REAL300000086837 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086837 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086837/0 /scratch/stefan/7769667/working/building/REAL300000086837 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/875 `/scratch/stefan/7769667/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1OCC1=CC=CC=C1) `REAL300000086837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086837 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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', '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, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 55, 55, 39, 55, 55, 55, 109, 201, 201, 201, 201, 201, 201, 21, 21, 21, 7, 1, 1, 1, 55, 55, 55, 55, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 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, 42, 43, 44]) total number of confs: 632 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: REAL300000086837 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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', '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, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 61, 61, 114, 201, 201, 201, 201, 201, 201, 201, 201, 43, 43, 43, 43, 43, 15, 3, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 114, 201, 201, 201, 43, 43, 43, 43, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 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]) total number of confs: 474 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086837 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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', '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, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 21, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 9, 27, 43, 43, 37, 43, 43, 7, 7, 7, 21, 55, 55, 55, 1, 1, 1, 1, 27, 27, 43, 43, 43, 43, 43] 201 rigid atoms, others: [1, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 237 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086837 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086837 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086837/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086837 Building REAL300000086838 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086838' /scratch/stefan/7769667/working/building/REAL300000086838 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086838 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086838/0 /scratch/stefan/7769667/working/building/REAL300000086838 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/876 `/scratch/stefan/7769667/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(NC(=O)C3=CC=C(Cl)C=C3)=CC=C2)C=N1) `REAL300000086838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086838 none O=C([O-])C1=CC=C(NN=CC2=CC(NC(=O)C3=CC=C(Cl)C=C3)=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 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: [2, 1, 2, 1, 1, 1, 1, 1, 10, 46, 46, 106, 106, 106, 201, 201, 201, 201, 201, 201, 201, 201, 201, 105, 105, 106, 1, 1, 1, 1, 10, 46, 106, 201, 201, 201, 201, 201, 105, 106, 106, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086838 none O=C([O-])C1=CC=C(NN=CC2=CC(NC(=O)C3=CC=C(Cl)C=C3)=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 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: [201, 201, 201, 201, 201, 201, 109, 49, 49, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 201, 201, 201, 201, 109, 49, 13, 3, 1, 1, 1, 1, 13, 13, 13, 201] 201 rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 458 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086838 none O=C([O-])C1=CC=C(NN=CC2=CC(NC(=O)C3=CC=C(Cl)C=C3)=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 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: [106, 106, 106, 106, 106, 106, 43, 8, 8, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 9, 9, 13, 13, 1, 1, 1, 106, 106, 106, 106, 42, 8, 1, 9, 13, 13, 13, 13, 1, 1, 1, 106] 201 rigid atoms, others: [32, 38, 39, 40, 9, 10, 11, 12, 13, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 41]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086838 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086838 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086838/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086838 Building REAL300000086839 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086839' /scratch/stefan/7769667/working/building/REAL300000086839 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086839 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086839/0 /scratch/stefan/7769667/working/building/REAL300000086839 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/877 `/scratch/stefan/7769667/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OCC2=CC=CC=C2)C=C1) `REAL300000086839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086839 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', '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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 102, 102, 51, 51, 147, 201, 201, 201, 201, 201, 201, 102, 102, 51, 51, 51, 11, 1, 1, 1, 102, 102, 201, 201, 201, 201, 201, 201, 201, 102, 102] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 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, 42, 43, 44]) total number of confs: 656 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086839 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', '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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 61, 61, 109, 201, 201, 201, 201, 201, 201, 201, 201, 22, 22, 22, 11, 3, 1, 1, 1, 1, 1, 1, 1, 22, 22, 61, 61, 61, 109, 201, 201, 201, 23, 23, 3, 3, 1, 1, 1, 1, 1, 23, 23] 201 rigid atoms, others: [38, 39, 40, 41, 42, 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, 43, 44]) total number of confs: 482 number of broken/clashed sets: 59 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086839 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', '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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 26, 102, 102, 102, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 2, 10, 22, 22, 10, 22, 22, 1, 1, 7, 7, 7, 26, 102, 102, 102, 1, 1, 10, 10, 23, 23, 10, 23, 23, 1, 1] 201 rigid atoms, others: [1, 34, 35, 43, 44, 13, 14, 15, 16, 17, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 245 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086839 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086839 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086839/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086839 Building REAL300000086840 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086840' /scratch/stefan/7769667/working/building/REAL300000086840 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086840 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086840/0 /scratch/stefan/7769667/working/building/REAL300000086840 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/878 `/scratch/stefan/7769667/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(N3CCCCC3)C([N+](=O)[O-])=C2)C=N1) `REAL300000086840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086840 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3CCCCC3)C([N+](=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 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, 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, 2, 1, 1, 1, 1, 1, 10, 43, 43, 64, 64, 62, 64, 64, 64, 64, 64, 64, 64, 64, 65, 65, 64, 1, 1, 1, 1, 10, 43, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 1] 65 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086840 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3CCCCC3)C([N+](=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 65, 65, 33, 12, 12, 2, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 3, 65, 65, 65, 64, 33, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 65] 65 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44]) total number of confs: 145 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086840 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3CCCCC3)C([N+](=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 65, 64, 32, 8, 8, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 2, 2, 1, 65, 65, 65, 64, 32, 8, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 65] 65 rigid atoms, others: [32, 43, 9, 10, 11, 12, 13, 14, 20, 21, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086840 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086840 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086840/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086840 Building REAL300000086841 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086841' /scratch/stefan/7769667/working/building/REAL300000086841 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086841 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086841/0 /scratch/stefan/7769667/working/building/REAL300000086841 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/879 `/scratch/stefan/7769667/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC(Br)=CC=C1O) `REAL300000086841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086841 none CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC(Br)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 232 conformations in input total number of sets (complete confs): 232 using faster count positions algorithm for large data unique positions, atoms: [86, 46, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 109, 109, 109, 80, 109, 109, 109, 86, 86, 86, 86, 86, 11, 1, 1, 1, 109, 109, 109, 218] 232 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 722 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086841 none CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC(Br)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 232 conformations in input total number of sets (complete confs): 232 using faster count positions algorithm for large data unique positions, atoms: [34, 12, 1, 12, 12, 50, 109, 109, 108, 108, 109, 109, 109, 109, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 50, 109, 109, 109, 1, 1, 1, 2] 232 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 329 number of broken/clashed sets: 87 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086841 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086841 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086841/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086841 Building REAL300000086842 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086842' /scratch/stefan/7769667/working/building/REAL300000086842 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086842 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086842/0 /scratch/stefan/7769667/working/building/REAL300000086842 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/880 `/scratch/stefan/7769667/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CN(CC3=CC=CC=C3)C3=CC=CC=C23)C=N1) `REAL300000086842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086842 none O=C([O-])C1=CC=C(NN=CC2=CN(CC3=CC=CC=C3)C3=CC=CC=C23)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 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] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 10, 24, 24, 60, 60, 60, 183, 201, 201, 201, 201, 201, 60, 60, 61, 61, 61, 60, 1, 1, 1, 1, 10, 24, 61, 183, 183, 201, 201, 201, 201, 201, 60, 61, 61, 61, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 652 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086842 none O=C([O-])C1=CC=C(NN=CC2=CN(CC3=CC=CC=C3)C3=CC=CC=C23)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 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, 115, 47, 47, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 201, 201, 201, 201, 115, 47, 16, 5, 5, 1, 1, 1, 1, 1, 16, 16, 16, 16, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44]) total number of confs: 459 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086842 none O=C([O-])C1=CC=C(NN=CC2=CN(CC3=CC=CC=C3)C3=CC=CC=C23)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 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] 0 hydrogens 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, 61, 61, 29, 6, 6, 1, 1, 1, 1, 1, 8, 16, 16, 10, 16, 16, 1, 1, 1, 1, 1, 1, 61, 61, 61, 60, 28, 6, 1, 8, 8, 16, 16, 10, 16, 16, 1, 1, 1, 1, 61] 201 rigid atoms, others: [32, 43, 40, 9, 10, 11, 12, 13, 41, 20, 21, 22, 23, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 44]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086842 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086842 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086842/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086842 Building REAL300000086843 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086843' /scratch/stefan/7769667/working/building/REAL300000086843 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086843 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086843/0 /scratch/stefan/7769667/working/building/REAL300000086843 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/881 `/scratch/stefan/7769667/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=CC(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=C1) `REAL300000086843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086843 none CC(=O)NC1=CC=CC(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 65, 169, 169, 169, 169, 169, 169, 169, 169, 1, 5, 5, 5, 5, 1, 1, 1, 13, 13, 13, 65, 169, 169, 169, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 22, 27, 28, 29, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 325 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086843 none CC(=O)NC1=CC=CC(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 169, 169, 169, 169, 169, 53, 53, 52, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 169, 201, 201, 201, 201, 169, 169, 169, 53, 53, 53, 11, 1, 1, 1, 169] 201 rigid atoms, others: [34, 35, 36, 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, 33, 37]) total number of confs: 357 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086843 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086843 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086843/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086843 Building REAL300000086844 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086844' /scratch/stefan/7769667/working/building/REAL300000086844 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086844 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086844/0 /scratch/stefan/7769667/working/building/REAL300000086844 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/882 `/scratch/stefan/7769667/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=C(Cl)C=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1) `REAL300000086844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086844 none CC1=NN(C2=CC=C(Cl)C=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 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 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 12, 60, 138, 138, 137, 137, 138, 138, 138, 138, 2, 2, 2, 5, 5, 5, 5, 12, 60, 138, 138, 138] 182 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]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086844 none CC1=NN(C2=CC=C(Cl)C=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 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 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 138, 138, 182, 182, 182, 182, 182, 182, 138, 138, 62, 62, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 182, 182, 182, 182, 62, 13, 1, 1, 1] 182 rigid atoms, others: [35, 36, 37, 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]) total number of confs: 284 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086844 none CC1=NN(C2=CC=C(Cl)C=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 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 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 40, 40, 101, 182, 182, 182, 182, 182, 182, 182, 182, 5, 5, 5, 1, 1, 1, 1, 40, 101, 182, 182, 182] 182 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 391 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086844 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086844 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086844/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086844 Building REAL300000086845 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086845' /scratch/stefan/7769667/working/building/REAL300000086845 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086845 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086845/0 /scratch/stefan/7769667/working/building/REAL300000086845 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/883 `/scratch/stefan/7769667/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1) `REAL300000086845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086845 none CC1=NN(C2=CC=CC=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 1, 1, 1, 12, 12, 58, 132, 132, 132, 132, 132, 132, 132, 132, 2, 2, 2, 5, 5, 1, 5, 5, 12, 58, 132, 132, 132] 171 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]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086845 none CC1=NN(C2=CC=CC=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 132, 132, 132, 171, 171, 132, 171, 171, 132, 132, 60, 60, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 171, 171, 132, 171, 171, 60, 13, 1, 1, 1] 171 rigid atoms, others: [35, 36, 37, 15, 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, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 384 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086845 none CC1=NN(C2=CC=CC=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 33, 33, 94, 171, 171, 171, 171, 171, 171, 171, 171, 5, 5, 5, 1, 1, 1, 1, 1, 33, 94, 171, 171, 171] 171 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37]) total number of confs: 363 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086845 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086845 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086845/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086845 Building REAL300000086846 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086846' /scratch/stefan/7769667/working/building/REAL300000086846 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086846 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086846/0 /scratch/stefan/7769667/working/building/REAL300000086846 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/884 `/scratch/stefan/7769667/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OC(F)F)C=C1) `REAL300000086846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086846 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [33, 34, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 84, 84, 34, 54, 186, 201, 201, 84, 84, 34, 34, 34, 7, 1, 1, 1, 84, 84, 201, 84, 84] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 537 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086846 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [6, 1, 6, 6, 28, 84, 84, 84, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 12, 42, 42, 1, 1, 6, 6, 6, 28, 84, 84, 84, 1, 1, 42, 1, 1] 201 rigid atoms, others: [1, 34, 33, 13, 14, 15, 16, 17, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 284 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086846 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086846 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086846/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086846 Building REAL300000086847 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086847' /scratch/stefan/7769667/working/building/REAL300000086847 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086847 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086847/0 /scratch/stefan/7769667/working/building/REAL300000086847 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/885 `/scratch/stefan/7769667/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C(=O)C3=CC=CC4=CC=CC2=C34)C=N1) `REAL300000086847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086847 none O=C([O-])C1=CC=C(NN=C2C(=O)C3=CC=CC4=CC=CC2=C34)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 12, 16, 16, 16, 16, 16, 16, 1] 17 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086847 none O=C([O-])C1=CC=C(NN=C2C(=O)C3=CC=CC4=CC=CC2=C34)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 17, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 16] 17 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 22, 23, 24, 25, 26]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086847 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086847 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086847/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086847 Building REAL300000086848 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086848' /scratch/stefan/7769667/working/building/REAL300000086848 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086848 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086848/0 /scratch/stefan/7769667/working/building/REAL300000086848 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/886 `/scratch/stefan/7769667/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2Br)C=N1) `REAL300000086848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086848 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2Br)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 38, 38, 49, 49, 47, 49, 49, 49, 1, 1, 1, 1, 12, 38, 49, 49, 49, 49, 1] 49 rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086848 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2Br)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 32, 8, 1, 1, 1, 1, 49] 49 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 27]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086848 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086848 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086848/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086848 Building REAL300000086849 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086849' /scratch/stefan/7769667/working/building/REAL300000086849 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086849 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086849/0 /scratch/stefan/7769667/working/building/REAL300000086849 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/887 `/scratch/stefan/7769667/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OC) `REAL300000086849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086849 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 12, 12, 12, 67, 169, 169, 169, 169, 169, 169, 169, 169, 1, 1, 1, 3, 4, 4, 4, 1, 1, 13, 13, 13, 67, 169, 169, 169, 1, 4, 4, 4] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 26, 27, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 338 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086849 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [201, 169, 169, 169, 169, 48, 48, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 169, 169, 169, 201, 201, 201, 201, 169, 169, 48, 48, 48, 11, 1, 1, 1, 169, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 357 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086849 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086849 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086849/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086849 Building REAL300000086850 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086850' /scratch/stefan/7769667/working/building/REAL300000086850 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086850 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086850/0 /scratch/stefan/7769667/working/building/REAL300000086850 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/888 `/scratch/stefan/7769667/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C(F)=C1) `REAL300000086850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086850 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 15, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 60, 149, 149, 149, 149, 149, 149, 149, 149, 1, 1, 1, 3, 3, 3, 1, 1, 13, 13, 13, 60, 149, 149, 149, 1] 149 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 19, 20, 21, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 282 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086850 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 15, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 61, 149, 149, 61, 61, 61, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 149, 149, 149, 149, 61, 61, 61, 13, 1, 1, 1, 149] 149 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 489 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086850 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086850 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086850/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086850 Building REAL300000086851 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086851' /scratch/stefan/7769667/working/building/REAL300000086851 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086851 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086851/0 /scratch/stefan/7769667/working/building/REAL300000086851 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/889 `/scratch/stefan/7769667/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])N=C1)C12CC3CC(CC(C3)C1)C2) `REAL300000086851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086851 none CC(N=NC1=CC=C(C(=O)[O-])N=C1)C12CC3CC(CC(C3)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 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: [19, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 19, 19, 19, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 27, 28, 29] set([0, 1, 2, 9, 10, 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, 41, 42, 43, 44]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086851 none CC(N=NC1=CC=C(C(=O)[O-])N=C1)C12CC3CC(CC(C3)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 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: [4, 1, 4, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 20 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086851 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086851 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086851/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086851 Building REAL300000086852 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086852' /scratch/stefan/7769667/working/building/REAL300000086852 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086852 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086852/0 /scratch/stefan/7769667/working/building/REAL300000086852 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/890 `/scratch/stefan/7769667/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC12CC3CC(CC(C3)C1)C2)N=NC1=CC=C(C(=O)[O-])N=C1) `REAL300000086852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086852 none CC(CC12CC3CC(CC(C3)C1)C2)N=NC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 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] 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, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26] 26 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 45, 46, 47]) total number of confs: 54 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086852 none CC(CC12CC3CC(CC(C3)C1)C2)N=NC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 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] 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, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [24, 9, 24, 24, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1] 26 rigid atoms, others: [45, 14, 15, 16, 17, 18, 19, 20, 46, 22, 23, 47, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 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: 77 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086852 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086852 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086852/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086852 Building REAL300000086853 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086853' /scratch/stefan/7769667/working/building/REAL300000086853 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086853 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086853/0 /scratch/stefan/7769667/working/building/REAL300000086853 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/891 `/scratch/stefan/7769667/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(Cl)N=C(NC3=CC=CC=C3)S2)C=N1) `REAL300000086853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086853 none O=C([O-])C1=CC=C(NN=CC2=C(Cl)N=C(NC3=CC=CC=C3)S2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 46, 46, 98, 98, 98, 98, 98, 200, 201, 201, 200, 201, 201, 98, 1, 1, 1, 1, 10, 46, 200, 201, 201, 200, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 472 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086853 none O=C([O-])C1=CC=C(NN=CC2=C(Cl)N=C(NC3=CC=CC=C3)S2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 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, 119, 64, 64, 27, 27, 27, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 27, 201, 201, 201, 201, 119, 64, 7, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 481 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086853 none O=C([O-])C1=CC=C(NN=CC2=C(Cl)N=C(NC3=CC=CC=C3)S2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 98, 98, 98, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 27, 27, 11, 27, 27, 1, 98, 98, 98, 98, 41, 11, 11, 27, 27, 11, 27, 27, 98] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 263 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086853 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086853 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086853/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086853 Building REAL300000086854 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086854' /scratch/stefan/7769667/working/building/REAL300000086854 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086854 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086854/0 /scratch/stefan/7769667/working/building/REAL300000086854 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/892 `/scratch/stefan/7769667/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(F)F) `REAL300000086854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086854 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [3, 1, 1, 1, 1, 1, 7, 7, 21, 62, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 9, 31, 31, 4, 4, 4, 1, 7, 21, 63, 63, 63, 1, 1, 30] 201 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 17, 18, 19, 20, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 35]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086854 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [118, 63, 63, 63, 28, 28, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 152, 201, 201, 118, 118, 118, 63, 28, 7, 1, 1, 1, 63, 63, 201] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 615 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086854 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086854 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086854/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086854 Building REAL300000086855 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086855' /scratch/stefan/7769667/working/building/REAL300000086855 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086855 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086855/0 /scratch/stefan/7769667/working/building/REAL300000086855 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/893 `/scratch/stefan/7769667/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC(Cl)=CC=C3Cl)O2)C=N1) `REAL300000086855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086855 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC(Cl)=CC=C3Cl)O2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 10, 56, 56, 108, 108, 108, 108, 201, 201, 201, 201, 201, 201, 201, 108, 1, 1, 1, 1, 10, 56, 108, 108, 201, 201, 201, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086855 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC(Cl)=CC=C3Cl)O2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 109, 36, 36, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 201, 201, 201, 201, 109, 36, 10, 10, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 431 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086855 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC(Cl)=CC=C3Cl)O2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 107, 107, 107, 107, 107, 36, 7, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 1, 107, 107, 107, 107, 36, 7, 1, 1, 10, 10, 10, 107] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086855 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086855 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086855/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086855 Building REAL300000086856 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086856' /scratch/stefan/7769667/working/building/REAL300000086856 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086856 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086856/0 /scratch/stefan/7769667/working/building/REAL300000086856 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/894 `/scratch/stefan/7769667/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OCCC(C)C)C=C1) `REAL300000086856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086856 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OCCC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 73, 73, 33, 51, 142, 155, 201, 201, 201, 73, 73, 33, 33, 33, 7, 1, 1, 1, 73, 73, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 73, 73] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 706 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086856 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OCCC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 26, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 6, 11, 19, 23, 23, 1, 1, 5, 5, 5, 26, 73, 73, 73, 1, 1, 11, 11, 19, 19, 23, 23, 23, 23, 23, 23, 23, 1, 1] 201 rigid atoms, others: [32, 1, 45, 33, 13, 14, 15, 16, 17, 46, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 233 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086856 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086856 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086856/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086856 Building REAL300000086857 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086857' /scratch/stefan/7769667/working/building/REAL300000086857 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086857 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086857/0 /scratch/stefan/7769667/working/building/REAL300000086857 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/895 `/scratch/stefan/7769667/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C2NC(=O)C(=NNC3=CC=C(C(=O)[O-])N=C3)C2=C1) `REAL300000086857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086857 none CC(C)C1=CC=C2NC(=O)C(=NNC3=CC=C(C(=O)[O-])N=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 27, 26, 26, 27, 27, 27, 27, 1, 1, 5, 5, 5, 4, 4, 4, 4, 1, 1, 1, 7, 27, 27, 27, 1] 31 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 33, 38, 31] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086857 none CC(C)C1=CC=C2NC(=O)C(=NNC3=CC=C(C(=O)[O-])N=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 27, 31, 27, 27, 27, 27, 27, 26, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 31, 31, 31, 31, 31, 31, 31, 27, 27, 26, 7, 1, 1, 1, 27] 31 rigid atoms, others: [35, 36, 37, 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, 33, 34, 38]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086857 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086857 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086857/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086857 Building REAL300000086858 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086858' /scratch/stefan/7769667/working/building/REAL300000086858 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086858 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086858/0 /scratch/stefan/7769667/working/building/REAL300000086858 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/896 `/scratch/stefan/7769667/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC=C3)N=C2C2=CC=CN=C2)C=N1) `REAL300000086858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086858 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC=C3)N=C2C2=CC=CN=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 102, 32, 32, 11, 11, 11, 11, 11, 16, 16, 11, 16, 16, 11, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 102, 32, 11, 16, 16, 11, 16, 16, 1, 1, 1, 1, 201] 201 rigid atoms, others: [39, 40, 41, 42, 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, 43]) total number of confs: 444 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086858 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC=C3)N=C2C2=CC=CN=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 12, 70, 70, 148, 148, 148, 149, 149, 148, 149, 149, 148, 148, 148, 201, 201, 201, 201, 201, 1, 1, 1, 1, 12, 70, 148, 149, 149, 148, 149, 149, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 43, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086858 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC=C3)N=C2C2=CC=CN=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 149, 149, 149, 149, 55, 14, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 149, 149, 149, 149, 55, 14, 4, 1, 1, 1, 1, 1, 16, 16, 16, 16, 149] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39, 40, 41, 42, 43]) total number of confs: 282 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086858 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC=C3)N=C2C2=CC=CN=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 148, 148, 49, 11, 11, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 1, 11, 11, 11, 11, 11, 148, 148, 148, 148, 49, 11, 1, 4, 4, 2, 4, 4, 11, 11, 11, 11, 148] 201 rigid atoms, others: [33, 9, 10, 11, 12, 13, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086858 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086858 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086858/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086858 Building REAL300000086859 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086859' /scratch/stefan/7769667/working/building/REAL300000086859 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086859 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086859/0 /scratch/stefan/7769667/working/building/REAL300000086859 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/897 `/scratch/stefan/7769667/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1) `REAL300000086859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086859 none CCCOC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 64, 159, 159, 159, 159, 159, 159, 159, 159, 1, 1, 17, 17, 17, 16, 16, 7, 7, 1, 1, 13, 13, 13, 64, 159, 159, 159, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 40, 21, 22, 30, 31] set([0, 1, 2, 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]) total number of confs: 374 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086859 none CCCOC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 193, 77, 35, 159, 159, 35, 35, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 159, 159, 201, 201, 201, 201, 201, 200, 201, 159, 159, 35, 35, 35, 7, 1, 1, 1, 159, 159] 201 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 661 number of broken/clashed sets: 75 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086859 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086859 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086859/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086859 Building REAL300000086860 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086860' /scratch/stefan/7769667/working/building/REAL300000086860 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086860 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086860/0 /scratch/stefan/7769667/working/building/REAL300000086860 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/898 `/scratch/stefan/7769667/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2=CC=C(C)C=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1) `REAL300000086860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086860 none CC1=NN(CC2=CC=C(C)C=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 8, 5, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 7, 14, 14, 9, 10, 14, 14, 1, 1, 1, 1, 7, 7, 29, 75, 75, 75, 75, 75, 75, 75, 75, 2, 2, 2, 7, 7, 14, 14, 14, 14, 14, 14, 14, 7, 28, 75, 75, 75] 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]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086860 none CC1=NN(CC2=CC=C(C)C=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 8, 5, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 75, 75, 75, 75, 187, 201, 201, 189, 201, 201, 201, 75, 75, 45, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 187, 187, 201, 201, 201, 201, 201, 201, 201, 45, 11, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 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, 37, 38, 39, 40]) total number of confs: 699 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086860 none CC1=NN(CC2=CC=C(C)C=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 8, 5, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 1, 13, 14, 13, 13, 46, 46, 94, 201, 201, 201, 201, 201, 201, 201, 201, 14, 14, 14, 4, 4, 1, 1, 2, 2, 2, 1, 1, 46, 94, 201, 201, 200] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 38, 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, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 459 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086860 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086860 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086860/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086860 Building REAL300000086861 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086861' /scratch/stefan/7769667/working/building/REAL300000086861 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086861 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086861/0 /scratch/stefan/7769667/working/building/REAL300000086861 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/899 `/scratch/stefan/7769667/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC1=CC=CO1) `REAL300000086861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086861 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 5, 1, 1, 1, 1, 12, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 28, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 2, 9, 9, 9, 9, 2, 2, 2, 1, 6, 28, 54, 54, 54, 2, 2, 2, 2, 2, 9, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086861 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 5, 1, 1, 1, 1, 12, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 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, 9, 9, 47, 47, 115, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 47, 115, 201, 201, 201, 9, 9, 9, 5, 5, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 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]) total number of confs: 472 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086861 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 5, 1, 1, 1, 1, 12, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 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, 32, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 82, 201, 201, 201, 201, 54, 54, 54, 54, 32, 9, 1, 1, 1, 54, 54, 54, 82, 82, 201, 201, 201] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 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: 425 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086861 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086861/1 /scratch/stefan/7769667/working/building/REAL300000086861 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/900 `/scratch/stefan/7769667/working/3D/900' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC1=CC=CO1) `REAL300000086861.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086861/1/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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086861 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 5, 1, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 25, 26, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 2, 9, 9, 9, 9, 2, 2, 2, 1, 8, 8, 47, 47, 47, 2, 2, 2, 2, 2, 9, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086861 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 5, 1, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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 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, 9, 9, 43, 108, 108, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 43, 43, 201, 201, 201, 9, 9, 9, 5, 5, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 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]) total number of confs: 427 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086861 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 5, 1, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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 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, 19, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 89, 201, 201, 201, 201, 47, 47, 47, 47, 19, 18, 1, 1, 1, 47, 47, 47, 89, 89, 201, 201, 201] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 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: 523 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086861 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086861 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086861/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086861/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086861 Building REAL300000086862 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086862' /scratch/stefan/7769667/working/building/REAL300000086862 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086862 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086862/0 /scratch/stefan/7769667/working/building/REAL300000086862 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/901 `/scratch/stefan/7769667/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OCC(C)C) `REAL300000086862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086862 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OCC(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7] 0 hydrogens 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, 6, 6, 14, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 9, 23, 29, 37, 3, 3, 3, 1, 1, 6, 14, 37, 37, 37, 1, 23, 23, 37, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 28, 29, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086862 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OCC(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7] 0 hydrogens 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, 37, 37, 37, 37, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 120, 183, 187, 201, 68, 68, 68, 37, 37, 15, 7, 1, 1, 1, 37, 183, 183, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 717 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086862 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086862 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086862/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086862 Building REAL300000086863 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086863' /scratch/stefan/7769667/working/building/REAL300000086863 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086863 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086863/0 /scratch/stefan/7769667/working/building/REAL300000086863 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/902 `/scratch/stefan/7769667/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1OC) `REAL300000086863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086863 none CCOC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 5, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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: [32, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 34, 95, 95, 95, 95, 95, 95, 95, 95, 1, 1, 4, 32, 32, 32, 32, 32, 1, 1, 1, 6, 34, 95, 95, 95, 4, 4, 4] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 21, 28, 29, 30] set([0, 1, 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]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086863 none CCOC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 5, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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: [201, 182, 95, 95, 95, 95, 95, 44, 44, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 95, 95, 138, 201, 201, 201, 201, 201, 95, 95, 95, 44, 11, 1, 1, 1, 138, 138, 138] 201 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 482 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086863 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086863 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086863/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086863 Building REAL300000086864 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086864' /scratch/stefan/7769667/working/building/REAL300000086864 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086864 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086864/0 /scratch/stefan/7769667/working/building/REAL300000086864 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/903 `/scratch/stefan/7769667/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC) `REAL300000086864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086864 none CCCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [59, 36, 10, 1, 1, 1, 1, 1, 7, 7, 15, 41, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 3, 63, 63, 63, 63, 63, 36, 36, 1, 7, 15, 42, 42, 42, 1, 1, 4, 4, 4] 201 rigid atoms, others: [3, 4, 5, 6, 7, 19, 20, 21, 22, 38, 37, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086864 none CCCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [201, 185, 135, 42, 42, 42, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 79, 201, 201, 201, 201, 201, 185, 185, 42, 17, 7, 1, 1, 1, 42, 42, 79, 79, 79] 201 rigid atoms, others: [34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 611 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086864 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086864 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086864/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086864 Building REAL300000086865 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086865' /scratch/stefan/7769667/working/building/REAL300000086865 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086865 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086865/0 /scratch/stefan/7769667/working/building/REAL300000086865 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/904 `/scratch/stefan/7769667/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(N2CCCCCC2)C=C1) `REAL300000086865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086865 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(N2CCCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 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: [61, 62, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 126, 126, 80, 109, 164, 164, 164, 164, 164, 164, 126, 126, 62, 62, 62, 13, 1, 1, 1, 126, 126, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 126, 126] 164 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 466 number of broken/clashed sets: 164 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086865 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(N2CCCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 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: [29, 5, 29, 29, 76, 164, 164, 164, 164, 164, 164, 164, 164, 2, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 29, 29, 29, 76, 164, 164, 164, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 164 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48]) total number of confs: 360 number of broken/clashed sets: 164 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086865 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(N2CCCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 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, 1, 7, 7, 37, 126, 126, 126, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 7, 7, 7, 37, 126, 126, 126, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1] 164 rigid atoms, others: [1, 34, 48, 33, 13, 14, 15, 16, 17, 24, 25, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 211 number of broken/clashed sets: 164 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086865 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086865 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086865/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086865 Building REAL300000086866 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086866' /scratch/stefan/7769667/working/building/REAL300000086866 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086866 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086866/0 /scratch/stefan/7769667/working/building/REAL300000086866 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/905 `/scratch/stefan/7769667/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OCC(N)=O) `REAL300000086866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086866 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OCC(N)=O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 11, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 9, 41, 98, 98, 3, 3, 3, 1, 1, 6, 11, 25, 25, 25, 1, 41, 41, 98, 98] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 28, 29, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086866 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OCC(N)=O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 25, 25, 25, 25, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 80, 172, 201, 201, 46, 46, 46, 25, 25, 11, 7, 1, 1, 1, 25, 172, 172, 201, 201] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 679 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086866 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086866 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086866/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086866 Building REAL300000086867 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086867' /scratch/stefan/7769667/working/building/REAL300000086867 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086867 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086867/0 /scratch/stefan/7769667/working/building/REAL300000086867 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/906 `/scratch/stefan/7769667/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)S2)C=N1) `REAL300000086867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086867 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)S2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 14, 1, 8, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 2, 1, 1, 1, 1, 1, 10, 34, 34, 50, 50, 50, 51, 51, 1, 1, 1, 1, 10, 34, 51, 50, 1] 51 rigid atoms, others: [1, 3, 4, 5, 6, 7, 16, 17, 18, 19, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086867 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)S2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 14, 1, 8, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 51, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 50, 20, 6, 1, 1, 51] 51 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086867 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086867 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086867/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086867 Building REAL300000086868 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086868' /scratch/stefan/7769667/working/building/REAL300000086868 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086868 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086868/0 /scratch/stefan/7769667/working/building/REAL300000086868 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/907 `/scratch/stefan/7769667/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(Cl)N=C3C=CC=CN32)C=N1) `REAL300000086868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086868 none O=C([O-])C1=CC=C(NN=CC2=C(Cl)N=C3C=CC=CN32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 12, 48, 48, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 12, 48, 63, 63, 63, 63, 1] 63 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086868 none O=C([O-])C1=CC=C(NN=CC2=C(Cl)N=C3C=CC=CN32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 29, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 29, 12, 1, 1, 1, 1, 63] 63 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 30]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086868 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086868 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086868/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086868 Building REAL300000086869 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086869' /scratch/stefan/7769667/working/building/REAL300000086869 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086869 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086869/0 /scratch/stefan/7769667/working/building/REAL300000086869 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/908 `/scratch/stefan/7769667/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(Cl)=C1OC) `REAL300000086869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086869 none CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 16, 1, 12, 5, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [33, 9, 1, 1, 1, 1, 1, 6, 6, 33, 96, 96, 95, 95, 96, 96, 96, 96, 1, 1, 1, 1, 1, 4, 33, 33, 33, 33, 33, 1, 6, 33, 96, 96, 96, 1, 4, 4, 4] 201 rigid atoms, others: [35, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086869 none CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 16, 1, 12, 5, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [201, 189, 96, 96, 96, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 150, 201, 201, 201, 201, 201, 96, 41, 11, 1, 1, 1, 96, 150, 150, 150] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 463 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086869 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086869 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086869/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086869 Building REAL300000086870 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086870' /scratch/stefan/7769667/working/building/REAL300000086870 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086870 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086870/0 /scratch/stefan/7769667/working/building/REAL300000086870 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/909 `/scratch/stefan/7769667/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC=CCC2=CC=CC=C2[N+](=O)[O-])C=N1) `REAL300000086870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086870 none O=C([O-])C1=CC=C(N=NC=CCC2=CC=CC=C2[N+](=O)[O-])C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 23, 23, 56, 63, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 23, 23, 56, 56, 68, 68, 68, 68, 1] 68 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086870 none O=C([O-])C1=CC=C(N=NC=CCC2=CC=CC=C2[N+](=O)[O-])C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 68, 68, 68, 39, 39, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 68, 68, 68, 68, 13, 13, 4, 4, 1, 1, 1, 1, 68] 68 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086870 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086870 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086870/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086870 Building REAL300000086871 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086871' /scratch/stefan/7769667/working/building/REAL300000086871 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086871 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086871/0 /scratch/stefan/7769667/working/building/REAL300000086871 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/910 `/scratch/stefan/7769667/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(F)C(F)=C(F)C(F)=C2F)C=N1) `REAL300000086871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086871 none O=C([O-])C1=CC=C(NN=CC2=C(F)C(F)=C(F)C(F)=C2F)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 15, 1, 15, 1, 15, 1, 15, 1, 8, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 42, 42, 50, 50, 50, 50, 42, 45, 50, 50, 50, 50, 1, 1, 1, 1, 12, 42, 1] 50 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086871 none O=C([O-])C1=CC=C(NN=CC2=C(F)C(F)=C(F)C(F)=C2F)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 15, 1, 15, 1, 15, 1, 15, 1, 8, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 49, 49, 49, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 25, 6, 49] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086871 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086871 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086871/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086871 Building REAL300000086872 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086872' /scratch/stefan/7769667/working/building/REAL300000086872 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086872 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086872/0 /scratch/stefan/7769667/working/building/REAL300000086872 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/911 `/scratch/stefan/7769667/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(C(F)(F)F)=C2)C=N1) `REAL300000086872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086872 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(C(F)(F)F)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 47, 47, 86, 86, 86, 86, 86, 87, 87, 87, 86, 1, 1, 1, 1, 10, 47, 86, 86, 86, 86, 1] 87 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086872 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(C(F)(F)F)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 86, 87, 86, 86, 86, 35, 10, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 86, 86, 86, 86, 35, 10, 1, 1, 1, 1, 86] 87 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 30]) total number of confs: 171 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086872 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086872 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086872/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086872 Building REAL300000086873 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086873' /scratch/stefan/7769667/working/building/REAL300000086873 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086873 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086873/0 /scratch/stefan/7769667/working/building/REAL300000086873 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/912 `/scratch/stefan/7769667/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(OC)=C1OC) `REAL300000086873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086873 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(OC)=C1OC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 11, 11, 33, 100, 100, 100, 100, 100, 100, 100, 100, 1, 1, 6, 1, 1, 6, 4, 4, 4, 1, 1, 11, 33, 100, 100, 100, 6, 6, 6, 6, 6, 6] 166 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 21, 22, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086873 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(OC)=C1OC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [141, 100, 100, 100, 100, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 100, 100, 142, 100, 100, 162, 141, 141, 141, 100, 100, 53, 11, 1, 1, 1, 142, 142, 142, 162, 162, 162] 166 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 410 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086873 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086873 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086873/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086873 Building REAL300000086874 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086874' /scratch/stefan/7769667/working/building/REAL300000086874 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086874 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086874/0 /scratch/stefan/7769667/working/building/REAL300000086874 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/913 `/scratch/stefan/7769667/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC1=CC=CC=C1) `REAL300000086874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086874 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7] 0 hydrogens 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, 11, 21, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 9, 36, 65, 65, 41, 65, 65, 3, 3, 3, 1, 5, 11, 22, 22, 22, 1, 1, 36, 36, 65, 65, 65, 65, 65] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 17, 18, 19, 20, 37, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086874 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7] 0 hydrogens 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, 65, 65, 65, 30, 65, 93, 93, 114, 201, 201, 201, 201, 201, 201, 201, 201, 65, 65, 15, 3, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 65, 93, 114, 201, 201, 201, 65, 65, 3, 3, 1, 1, 1, 1, 1] 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]) total number of confs: 637 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086874 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 22, 22, 22, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 82, 181, 201, 201, 189, 201, 201, 42, 42, 42, 22, 9, 5, 1, 1, 1, 22, 22, 181, 181, 201, 201, 201, 201, 201] 201 rigid atoms, others: [34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 677 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086874 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086874 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086874/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086874 Building REAL300000086875 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086875' /scratch/stefan/7769667/working/building/REAL300000086875 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086875 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086875/0 /scratch/stefan/7769667/working/building/REAL300000086875 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/914 `/scratch/stefan/7769667/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC#N)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1) `REAL300000086875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086875 none CN(CCC#N)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 5, 5, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 3, 10, 14, 14, 1, 1, 1, 1, 1, 6, 6, 32, 89, 89, 88, 88, 89, 89, 89, 89, 1, 1, 3, 3, 3, 10, 10, 14, 14, 1, 1, 6, 32, 89, 89, 89, 1, 1] 201 rigid atoms, others: [32, 1, 38, 6, 7, 8, 9, 10, 39, 22, 23, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 229 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086875 none CN(CCC#N)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 5, 5, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 66, 126, 191, 201, 201, 65, 89, 89, 39, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 89, 89, 126, 126, 126, 191, 191, 201, 201, 89, 89, 39, 11, 1, 1, 1, 89, 89] 201 rigid atoms, others: [35, 36, 37, 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, 33, 34, 38, 39]) total number of confs: 814 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086875 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086875 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086875/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086875 Building REAL300000086876 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086876' /scratch/stefan/7769667/working/building/REAL300000086876 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086876 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086876/0 /scratch/stefan/7769667/working/building/REAL300000086876 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/915 `/scratch/stefan/7769667/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1O) `REAL300000086876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086876 none COC1=CC(Br)=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 36, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1, 4, 4, 4, 1, 1, 9, 36, 88, 88, 88, 2] 176 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 25, 26] set([0, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 173 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086876 none COC1=CC(Br)=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [88, 88, 88, 88, 88, 88, 88, 59, 59, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 88, 88, 88, 59, 13, 1, 1, 1, 176] 176 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 308 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086876 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086876 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086876/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086876 Building REAL300000086877 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086877' /scratch/stefan/7769667/working/building/REAL300000086877 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086877 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086877/0 /scratch/stefan/7769667/working/building/REAL300000086877 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/916 `/scratch/stefan/7769667/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=C1)CCCC2=NNC1=CC=C(C(=O)[O-])N=C1) `REAL300000086877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086877 none COC1=CC=C2C(=C1)CCCC2=NNC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 39, 39, 39] 39 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 65 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086877 none COC1=CC=C2C(=C1)CCCC2=NNC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 11, 1, 1, 1] 39 rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 57 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086877 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086877 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086877/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086877 Building REAL300000086878 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086878' /scratch/stefan/7769667/working/building/REAL300000086878 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086878 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086878/0 /scratch/stefan/7769667/working/building/REAL300000086878 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/917 `/scratch/stefan/7769667/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(C)=C1) `REAL300000086878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086878 none CCN(CCO)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [27, 11, 1, 11, 23, 35, 1, 1, 1, 1, 1, 6, 6, 20, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 27, 27, 27, 27, 27, 23, 23, 35, 35, 105, 1, 1, 6, 20, 55, 55, 55, 2, 2, 2, 1] 603 rigid atoms, others: [2, 35, 36, 6, 7, 8, 9, 10, 45, 22, 23, 24] set([0, 1, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 420 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086878 none CCN(CCO)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [185, 138, 27, 136, 183, 187, 27, 55, 55, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 185, 185, 185, 185, 185, 183, 183, 187, 187, 561, 55, 55, 27, 7, 1, 1, 1, 55, 55, 55, 55] 603 rigid atoms, others: [39, 40, 41, 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, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 1463 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086878 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086878 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086878/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086878 Building REAL300000086879 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086879' /scratch/stefan/7769667/working/building/REAL300000086879 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086879 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086879/0 /scratch/stefan/7769667/working/building/REAL300000086879 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/918 `/scratch/stefan/7769667/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1[N+](=O)[O-]) `REAL300000086879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086879 none CN(C1=CC=CC=C1)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 8, 11, 11, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 24, 24, 42, 72, 72, 72, 72, 72, 72, 72, 72, 6, 6, 6, 7, 7, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 24, 42, 72, 72, 72, 6] 72 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 34, 35, 36, 33] set([0, 8, 9, 10, 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]) total number of confs: 178 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: REAL300000086879 none CN(C1=CC=CC=C1)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 8, 11, 11, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [49, 24, 49, 72, 72, 72, 72, 72, 31, 48, 48, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 72, 49, 49, 72, 72, 72, 72, 72, 48, 48, 24, 7, 1, 1, 1, 48] 72 rigid atoms, others: [41, 42, 43, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44]) total number of confs: 290 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086879 none CN(C1=CC=CC=C1)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 8, 11, 11, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 6, 7, 2, 6, 6, 1, 1, 1, 1, 1, 6, 6, 21, 48, 48, 47, 48, 48, 48, 48, 48, 1, 1, 1, 2, 2, 3, 3, 3, 6, 7, 3, 6, 6, 1, 1, 6, 21, 48, 48, 48, 1] 72 rigid atoms, others: [1, 37, 38, 8, 9, 10, 11, 12, 44, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 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]) total number of confs: 137 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086879 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086879 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086879/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086879 Building REAL300000086880 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086880' /scratch/stefan/7769667/working/building/REAL300000086880 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086880 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086880/0 /scratch/stefan/7769667/working/building/REAL300000086880 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/919 `/scratch/stefan/7769667/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C=C1) `REAL300000086880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086880 none CCCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [163, 149, 56, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 143, 143, 96, 143, 143, 143, 170, 170, 170, 170, 170, 149, 149, 11, 1, 1, 1, 143, 143, 143, 143] 181 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 973 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086880 none CCCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [36, 24, 7, 1, 7, 7, 38, 143, 143, 143, 143, 143, 143, 143, 143, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 24, 24, 38, 143, 143, 143, 1, 1, 1, 1] 181 rigid atoms, others: [33, 34, 3, 36, 35, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 368 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086880 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086880 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086880/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086880 Building REAL300000086881 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086881' /scratch/stefan/7769667/working/building/REAL300000086881 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086881 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086881/0 /scratch/stefan/7769667/working/building/REAL300000086881 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/920 `/scratch/stefan/7769667/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C1CCC(N=NC2=CC=C(C(=O)[O-])N=C2)CC1) `REAL300000086881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086881 none CCC(C)(C)C1CCC(N=NC2=CC=C(C(=O)[O-])N=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 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: [5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 6, 6, 6, 5, 5, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 21, 21, 21, 1, 1, 1, 1] 53 rigid atoms, others: [33, 2, 35, 36, 5, 6, 7, 8, 9, 42, 43, 44, 34, 45, 20, 21, 38, 37] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086881 none CCC(C)(C)C1CCC(N=NC2=CC=C(C(=O)[O-])N=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 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, 30, 21, 29, 29, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 53, 53, 53, 53, 53, 51, 51, 29, 51, 29, 51, 21, 21, 21, 21, 21, 21, 1, 1, 1, 21, 21, 21, 21] 53 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 421 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086881 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086881 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086881/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086881 Building REAL300000086882 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086882' /scratch/stefan/7769667/working/building/REAL300000086882 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086882 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086882/0 /scratch/stefan/7769667/working/building/REAL300000086882 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/921 `/scratch/stefan/7769667/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=C3OCOC3=C2)C=N1) `REAL300000086882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086882 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=C3OCOC3=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 12, 5, 12, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 11, 37, 37, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 11, 37, 70, 70, 70, 70, 1] 70 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086882 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=C3OCOC3=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 12, 5, 12, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 70, 70, 70, 31, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 31, 11, 1, 1, 1, 1, 70] 70 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 30]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086882 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086882 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086882/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086882 Building REAL300000086883 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086883' /scratch/stefan/7769667/working/building/REAL300000086883 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086883 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086883/0 /scratch/stefan/7769667/working/building/REAL300000086883 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/922 `/scratch/stefan/7769667/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(OC(F)F)C=CC3=CC=CC=C32)C=N1) `REAL300000086883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086883 none O=C([O-])C1=CC=C(NN=CC2=C(OC(F)F)C=CC3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 6, 36, 36, 96, 96, 187, 201, 201, 96, 96, 96, 96, 96, 96, 96, 96, 1, 1, 1, 1, 6, 36, 201, 96, 96, 96, 96, 96, 96, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26, 27, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086883 none O=C([O-])C1=CC=C(NN=CC2=C(OC(F)F)C=CC3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 96, 96, 96, 96, 96, 39, 11, 11, 1, 1, 1, 1, 9, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 39, 11, 30, 1, 1, 1, 1, 1, 1, 96] 201 rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086883 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086883 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086883/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086883 Building REAL300000086884 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086884' /scratch/stefan/7769667/working/building/REAL300000086884 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086884 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086884/0 /scratch/stefan/7769667/working/building/REAL300000086884 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/923 `/scratch/stefan/7769667/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OC(F)F)C=C1)N=NC1=CC=C(C(=O)[O-])N=C1) `REAL300000086884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086884 none CC(CCC1=CC=C(OC(F)F)C=C1)N=NC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 7, 7, 7, 3, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 1, 1, 12, 31, 31, 1, 1, 9, 34, 34, 82, 82, 82, 82, 82, 82, 82, 82, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 31, 1, 1, 82, 82, 82] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 12, 13, 34, 36, 37, 31] set([0, 1, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 38, 39, 40]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086884 none CC(CCC1=CC=C(OC(F)F)C=C1)N=NC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 7, 7, 7, 3, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 7, 35, 73, 82, 82, 82, 82, 82, 180, 201, 201, 82, 82, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 79, 79, 79, 82, 82, 82, 201, 82, 82, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 15, 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, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 605 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086884 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086884 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086884/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086884 Building REAL300000086885 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086885' /scratch/stefan/7769667/working/building/REAL300000086885 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086885 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086885/0 /scratch/stefan/7769667/working/building/REAL300000086885 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/924 `/scratch/stefan/7769667/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC(Cl)=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1) `REAL300000086885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086885 none CC1=NN(C2=CC=CC(Cl)=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 16, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 4, 11, 11, 11, 1, 1, 1, 1, 7, 7, 35, 81, 81, 81, 81, 81, 81, 81, 81, 2, 2, 2, 11, 11, 10, 11, 7, 35, 81, 81, 81] 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]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086885 none CC1=NN(C2=CC=CC(Cl)=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 16, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 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 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, 81, 201, 201, 201, 201, 201, 201, 81, 81, 39, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 201, 201, 201, 201, 39, 11, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 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]) total number of confs: 299 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086885 none CC1=NN(C2=CC=CC(Cl)=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 16, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 39, 39, 97, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 11, 1, 1, 1, 1, 39, 97, 201, 201, 201] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 430 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086885 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086885 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086885/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086885 Building REAL300000086886 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086886' /scratch/stefan/7769667/working/building/REAL300000086886 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086886 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086886/0 /scratch/stefan/7769667/working/building/REAL300000086886 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/925 `/scratch/stefan/7769667/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])N=C3)O2)C=C1) `REAL300000086886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086886 none COC(=O)C1=CC=C(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])N=C3)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'O.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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 12, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 12, 12, 32, 32, 106, 201, 201, 201, 201, 201, 201, 201, 201, 12, 1, 1, 7, 7, 7, 1, 1, 12, 12, 32, 106, 201, 201, 201, 1, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 39, 40, 25, 26, 30, 31] set([0, 1, 3, 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]) total number of confs: 442 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086886 none COC(=O)C1=CC=C(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])N=C3)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'O.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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 12, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 196, 201, 72, 201, 201, 71, 71, 71, 71, 37, 37, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 201, 201, 71, 71, 37, 11, 1, 1, 1, 201, 201] 201 rigid atoms, others: [36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 704 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086886 none COC(=O)C1=CC=C(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])N=C3)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'O.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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 12, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 26, 2, 20, 1, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 30, 71, 71, 71, 71, 71, 71, 71, 71, 1, 12, 12, 30, 30, 30, 12, 12, 1, 1, 7, 30, 71, 71, 71, 12, 12] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 24] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086886 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086886 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086886/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086886 Building REAL300000086887 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086887' /scratch/stefan/7769667/working/building/REAL300000086887 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086887 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086887/0 /scratch/stefan/7769667/working/building/REAL300000086887 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/926 `/scratch/stefan/7769667/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(C)C) `REAL300000086887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086887 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens 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, 7, 7, 34, 93, 94, 94, 94, 94, 94, 94, 94, 1, 1, 1, 1, 9, 21, 21, 4, 4, 4, 1, 7, 34, 94, 94, 94, 1, 1, 21, 21, 21, 21, 21, 21, 21] 201 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 17, 18, 19, 20, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 240 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086887 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens 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, 94, 94, 94, 33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 196, 201, 201, 158, 158, 158, 94, 33, 9, 1, 1, 1, 94, 94, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 438 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086887 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086887 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086887/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086887 Building REAL300000086888 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086888' /scratch/stefan/7769667/working/building/REAL300000086888 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086888 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086888/0 /scratch/stefan/7769667/working/building/REAL300000086888 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/927 `/scratch/stefan/7769667/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OCC) `REAL300000086888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086888 none CCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens 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, 36, 9, 1, 1, 1, 1, 1, 1, 4, 4, 10, 23, 23, 22, 22, 23, 23, 23, 23, 1, 1, 1, 9, 25, 69, 69, 69, 68, 68, 36, 36, 1, 1, 4, 10, 23, 23, 23, 1, 25, 25, 25, 25, 25] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 39, 20, 21, 22] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 453 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086888 none CCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 161, 89, 23, 23, 23, 23, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 76, 98, 191, 191, 191, 191, 191, 161, 161, 23, 23, 11, 7, 1, 1, 1, 23, 98, 98, 98, 98, 98] 201 rigid atoms, others: [36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44]) total number of confs: 859 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086888 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086888 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086888/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086888 Building REAL300000086889 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086889' /scratch/stefan/7769667/working/building/REAL300000086889 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086889 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086889/0 /scratch/stefan/7769667/working/building/REAL300000086889 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/928 `/scratch/stefan/7769667/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C([N+](=O)[O-])C=C32)C=N1) `REAL300000086889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086889 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C([N+](=O)[O-])C=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 21, 21, 20, 20, 1, 1, 1, 1, 12, 20, 20, 20, 20, 1] 21 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086889 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C([N+](=O)[O-])C=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 20, 20, 20, 7, 1, 1, 1, 1, 20] 21 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 22, 23, 24, 25, 26, 31]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086889 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086889 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086889/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086889 Building REAL300000086890 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086890' /scratch/stefan/7769667/working/building/REAL300000086890 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086890 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086890/0 /scratch/stefan/7769667/working/building/REAL300000086890 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/929 `/scratch/stefan/7769667/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(Br)C=C32)C=N1) `REAL300000086890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086890 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(Br)C=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 12, 20, 20, 20, 20, 1] 21 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086890 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(Br)C=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 7, 1, 1, 1, 1, 20] 21 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 29]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086890 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086890 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086890/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086890 Building REAL300000086891 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086891' /scratch/stefan/7769667/working/building/REAL300000086891 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086891 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086891/0 /scratch/stefan/7769667/working/building/REAL300000086891 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/930 `/scratch/stefan/7769667/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C(=O)NC3=C(Cl)C=C(Cl)C=C23)C=N1) `REAL300000086891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086891 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=C(Cl)C=C(Cl)C=C23)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 16, 1, 1, 16, 1, 1, 1, 8, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 12, 20, 20, 20, 1] 21 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086891 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=C(Cl)C=C(Cl)C=C23)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 16, 1, 1, 16, 1, 1, 1, 8, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 7, 1, 1, 1, 20] 21 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 29]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086891 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086891 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086891/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086891 Building REAL300000086892 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086892' /scratch/stefan/7769667/working/building/REAL300000086892 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086892 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086892/0 /scratch/stefan/7769667/working/building/REAL300000086892 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/931 `/scratch/stefan/7769667/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C(=O)N(CC3=CC=CC=C3)C3=CC=CC=C32)C=N1) `REAL300000086892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086892 none O=C([O-])C1=CC=C(NN=C2C(=O)N(CC3=CC=CC=C3)C3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 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 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 44, 44, 44, 44, 44, 122, 122, 122, 122, 122, 122, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 10, 122, 122, 122, 122, 122, 122, 122, 44, 44, 44, 44, 1] 123 rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086892 none O=C([O-])C1=CC=C(NN=C2C(=O)N(CC3=CC=CC=C3)C3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 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 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [123, 122, 123, 122, 122, 122, 49, 12, 12, 12, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 122, 122, 122, 122, 49, 3, 3, 1, 1, 1, 1, 1, 12, 12, 12, 12, 122] 123 rigid atoms, others: [33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42]) total number of confs: 245 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086892 none O=C([O-])C1=CC=C(NN=C2C(=O)N(CC3=CC=CC=C3)C3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 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 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [45, 44, 45, 44, 44, 44, 7, 1, 1, 1, 1, 1, 1, 1, 6, 12, 12, 7, 12, 12, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 7, 6, 6, 12, 12, 12, 12, 12, 1, 1, 1, 1, 44] 123 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 40, 41, 20, 21, 22, 23, 24, 25, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 110 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086892 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086892 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086892/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086892 Building REAL300000086893 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086893' /scratch/stefan/7769667/working/building/REAL300000086893 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086893 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086893/0 /scratch/stefan/7769667/working/building/REAL300000086893 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/932 `/scratch/stefan/7769667/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1) `REAL300000086893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086893 none CCCCCCCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [46, 46, 39, 28, 21, 13, 5, 3, 1, 1, 1, 1, 1, 1, 6, 6, 12, 33, 33, 32, 33, 33, 33, 33, 33, 1, 1, 55, 55, 55, 55, 55, 54, 54, 44, 44, 31, 31, 21, 21, 13, 13, 5, 5, 1, 1, 6, 12, 33, 33, 33, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 44, 45, 12, 13, 51, 52, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50]) total number of confs: 443 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086893 none CCCCCCCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [186, 186, 174, 150, 138, 122, 74, 53, 21, 15, 33, 33, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 201, 201, 201, 201, 201, 201, 201, 182, 182, 158, 158, 138, 138, 122, 122, 70, 70, 33, 33, 15, 7, 1, 1, 1, 33, 33] 201 rigid atoms, others: [48, 49, 50, 15, 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, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 51, 52]) total number of confs: 1061 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086893 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086893 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086893/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086893 Building REAL300000086894 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086894' /scratch/stefan/7769667/working/building/REAL300000086894 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086894 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086894/0 /scratch/stefan/7769667/working/building/REAL300000086894 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/933 `/scratch/stefan/7769667/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C2=CC=CC=C2C(C)(C)C1C=CN=NC1=CC=C(C(=O)[O-])N=C1) `REAL300000086894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086894 none CN1C2=CC=CC=C2C(C)(C)C1C=CN=NC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 2, 2, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 38, 28, 29, 30, 31] set([13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086894 none CN1C2=CC=CC=C2C(C)(C)C1C=CN=NC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 1, 1, 1] 13 rigid atoms, others: [41, 42, 43, 15, 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, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 28 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086894 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086894 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086894/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086894 Building REAL300000086895 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086895' /scratch/stefan/7769667/working/building/REAL300000086895 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086895 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086895/0 /scratch/stefan/7769667/working/building/REAL300000086895 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/934 `/scratch/stefan/7769667/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(O)C=CC3=CC=CC=C32)C=N1) `REAL300000086895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086895 none O=C([O-])C1=CC=C(NN=CC2=C(O)C=CC3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 51, 51, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 1, 1, 1, 1, 12, 51, 200, 100, 100, 100, 100, 100, 100, 1] 200 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 350 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086895 none O=C([O-])C1=CC=C(NN=CC2=C(O)C=CC3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 100, 48, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 48, 11, 2, 1, 1, 1, 1, 1, 1, 100] 200 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 204 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086895 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086895 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086895/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086895 Building REAL300000086896 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086896' /scratch/stefan/7769667/working/building/REAL300000086896 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086896 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086896/0 /scratch/stefan/7769667/working/building/REAL300000086896 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/935 `/scratch/stefan/7769667/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C3C=CC=CC3=CC3=CC=CC=C32)C=N1) `REAL300000086896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086896 none O=C([O-])C1=CC=C(NN=CC2=C3C=CC=CC3=CC3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 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, 2, 1, 1, 1, 1, 1, 12, 42, 42, 63, 63, 63, 63, 63, 63, 52, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 12, 42, 63, 63, 63, 63, 52, 63, 63, 63, 63, 1] 63 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086896 none O=C([O-])C1=CC=C(NN=CC2=C3C=CC=CC3=CC3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63] 63 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 24, 25, 26, 27, 28, 29]) total number of confs: 127 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086896 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086896 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086896/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086896 Building REAL300000086897 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086897' /scratch/stefan/7769667/working/building/REAL300000086897 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086897 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086897/0 /scratch/stefan/7769667/working/building/REAL300000086897 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/936 `/scratch/stefan/7769667/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(OCC3=CC=CC=C3)C=C2)C=N1) `REAL300000086897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086897 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OCC3=CC=CC=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 56, 56, 92, 92, 58, 61, 134, 178, 178, 178, 178, 178, 178, 92, 92, 1, 1, 1, 1, 12, 56, 92, 93, 178, 178, 178, 178, 178, 178, 178, 92, 92, 1] 179 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 534 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086897 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OCC3=CC=CC=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 179, 179, 178, 97, 50, 50, 11, 11, 22, 22, 11, 3, 1, 1, 1, 1, 1, 1, 1, 22, 22, 179, 179, 179, 178, 97, 50, 22, 22, 3, 3, 1, 1, 1, 1, 1, 22, 22, 179] 179 rigid atoms, others: [34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 460 number of broken/clashed sets: 54 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086897 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OCC3=CC=CC=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 93, 93, 42, 5, 5, 1, 1, 1, 1, 1, 1, 2, 10, 22, 22, 10, 22, 22, 1, 1, 93, 93, 93, 92, 42, 5, 1, 1, 10, 10, 22, 22, 10, 22, 22, 1, 1, 93] 179 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 247 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086897 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086897 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086897/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086897 Building REAL300000086898 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086898' /scratch/stefan/7769667/working/building/REAL300000086898 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086898 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086898/0 /scratch/stefan/7769667/working/building/REAL300000086898 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/937 `/scratch/stefan/7769667/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1Br) `REAL300000086898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086898 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [48, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 75, 75, 75, 75, 75, 75, 49, 49, 49, 11, 1, 1, 1, 75, 75, 75, 75] 75 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086898 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 25, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 25, 75, 75, 75, 1, 1, 1, 1] 75 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 129 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086898 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086898 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086898/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086898 Building REAL300000086899 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086899' /scratch/stefan/7769667/working/building/REAL300000086899 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086899 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086899/0 /scratch/stefan/7769667/working/building/REAL300000086899 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/938 `/scratch/stefan/7769667/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Br)C=C1C=NNC1=CC=C(C(=O)[O-])N=C1) `REAL300000086899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086899 none COC1=CC=C(Br)C=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 42, 109, 109, 108, 108, 109, 109, 109, 109, 4, 4, 4, 1, 1, 1, 12, 42, 109, 109, 109] 109 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086899 none COC1=CC=C(Br)C=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 109, 84, 109, 109, 109, 74, 74, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 109, 109, 74, 13, 1, 1, 1] 109 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086899 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086899 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086899/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086899 Building REAL300000086900 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086900' /scratch/stefan/7769667/working/building/REAL300000086900 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086900 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086900/0 /scratch/stefan/7769667/working/building/REAL300000086900 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/939 `/scratch/stefan/7769667/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(Br)=C1O) `REAL300000086900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086900 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(Br)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 10, 10, 53, 129, 129, 128, 128, 129, 129, 129, 129, 1, 1, 1, 1, 1, 4, 4, 4, 1, 10, 53, 129, 129, 129, 1, 2] 258 rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 25, 31] set([0, 32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086900 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(Br)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 129, 67, 67, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 129, 129, 129, 129, 129, 67, 13, 1, 1, 1, 129, 258] 258 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 454 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086900 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086900 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086900/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086900 Building REAL300000086901 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086901' /scratch/stefan/7769667/working/building/REAL300000086901 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086901 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086901/0 /scratch/stefan/7769667/working/building/REAL300000086901 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/940 `/scratch/stefan/7769667/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(Cl)C([N+](=O)[O-])=C2)C=N1) `REAL300000086901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086901 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Cl)C([N+](=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 11, 43, 43, 73, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1, 11, 43, 73, 73, 73, 1] 73 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086901 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Cl)C([N+](=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 73, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 73, 73, 73, 73, 31, 9, 1, 1, 1, 73] 73 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086901 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086901 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086901/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086901 Building REAL300000086902 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086902' /scratch/stefan/7769667/working/building/REAL300000086902 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086902 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086902/0 /scratch/stefan/7769667/working/building/REAL300000086902 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/941 `/scratch/stefan/7769667/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C2CCCCC2)C=C1) `REAL300000086902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086902 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [56, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 101, 101, 57, 57, 156, 156, 156, 156, 156, 101, 101, 57, 57, 57, 11, 1, 1, 1, 101, 101, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 101, 101] 156 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 575 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: REAL300000086902 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 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: [14, 2, 14, 16, 61, 156, 156, 156, 156, 156, 156, 156, 156, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 14, 17, 16, 61, 156, 156, 156, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 156 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, 45, 46]) total number of confs: 332 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086902 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 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: [6, 1, 6, 6, 27, 101, 101, 101, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 6, 6, 6, 27, 101, 101, 101, 1, 1, 10, 10, 10, 10, 10, 10, 11, 10, 10, 10, 10, 1, 1] 156 rigid atoms, others: [32, 1, 45, 33, 13, 14, 15, 16, 17, 46, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 185 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086902 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086902 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086902/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086902 Building REAL300000086903 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086903' /scratch/stefan/7769667/working/building/REAL300000086903 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086903 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086903/0 /scratch/stefan/7769667/working/building/REAL300000086903 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/942 `/scratch/stefan/7769667/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C(Cl)=C1) `REAL300000086903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086903 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [60, 61, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 105, 105, 105, 105, 105, 105, 105, 61, 61, 61, 11, 1, 1, 1, 105, 105, 105] 105 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086903 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 41, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 41, 105, 105, 105, 1, 1, 1] 105 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 191 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086903 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086903 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086903/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086903 Building REAL300000086904 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086904' /scratch/stefan/7769667/working/building/REAL300000086904 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086904 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086904/0 /scratch/stefan/7769667/working/building/REAL300000086904 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/943 `/scratch/stefan/7769667/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3)C=C2)C=N1) `REAL300000086904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086904 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 50, 50, 54, 54, 50, 50, 55, 55, 50, 55, 55, 54, 54, 1, 1, 1, 1, 12, 50, 54, 54, 55, 55, 55, 55, 55, 55, 55, 1] 55 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 37] set([0, 2, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086904 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 55, 19, 9, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 55, 55, 55, 55, 19, 9, 3, 3, 1, 1, 1, 1, 1, 3, 3, 55] 55 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 109 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086904 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 54, 14, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 55, 55, 55, 54, 14, 4, 1, 1, 3, 3, 1, 3, 3, 1, 1, 55] 55 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 37]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086904 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086904 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086904/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086904 Building REAL300000086905 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086905' /scratch/stefan/7769667/working/building/REAL300000086905 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086905 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086905/0 /scratch/stefan/7769667/working/building/REAL300000086905 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/944 `/scratch/stefan/7769667/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(Cl)=C1) `REAL300000086905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086905 none CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 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: [93, 54, 55, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 155, 155, 150, 155, 155, 155, 93, 93, 93, 93, 93, 11, 1, 1, 1, 155, 155, 155, 155] 183 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 33, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 456 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086905 none CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 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: [39, 13, 1, 13, 13, 58, 155, 155, 155, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 58, 155, 155, 155, 1, 1, 1, 1] 183 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 397 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086905 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086905 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086905/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086905 Building REAL300000086906 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086906' /scratch/stefan/7769667/working/building/REAL300000086906 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086906 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086906/0 /scratch/stefan/7769667/working/building/REAL300000086906 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/945 `/scratch/stefan/7769667/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C2C=C1) `REAL300000086906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086906 none COC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 12, 12, 85, 168, 168, 168, 168, 168, 168, 168, 168, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 85, 168, 168, 168, 1, 1, 1, 1, 1, 1] 168 rigid atoms, others: [32, 1, 2, 3, 4, 37, 35, 33, 34, 16, 17, 18, 19, 20, 21, 22, 23, 36] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086906 none COC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 63, 63, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 168, 168, 168, 168, 168, 168, 168, 63, 12, 1, 1, 1, 168, 168, 168, 168, 168, 168] 168 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086906 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086906 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086906/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086906 Building REAL300000086907 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086907' /scratch/stefan/7769667/working/building/REAL300000086907 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086907 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086907/0 /scratch/stefan/7769667/working/building/REAL300000086907 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/946 `/scratch/stefan/7769667/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])N=C1) `REAL300000086907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086907 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [52, 32, 52, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 38, 38, 38, 38, 38, 38, 38, 38, 32, 32, 1, 1, 1, 1, 4, 12, 38, 38, 38] 103 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086907 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 76, 38, 38, 38, 21, 38, 38, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 103, 38, 38, 38, 38, 21, 8, 1, 1, 1] 103 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 339 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086907 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086907 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086907/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086907 Building REAL300000086908 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086908' /scratch/stefan/7769667/working/building/REAL300000086908 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086908 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086908/0 /scratch/stefan/7769667/working/building/REAL300000086908 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/947 `/scratch/stefan/7769667/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=CC=C(C(C)=NNC3=CC=C(C(=O)[O-])N=C3)C=C2C=C1) `REAL300000086908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086908 none COC1=CC2=CC=C(C(C)=NNC3=CC=C(C(=O)[O-])N=C3)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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 12, 12, 12, 67, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 13, 13, 13, 67, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 39, 40, 21, 22, 23, 24, 38, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 357 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086908 none COC1=CC2=CC=C(C(C)=NNC3=CC=C(C(=O)[O-])N=C3)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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 65, 65, 65, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 65, 65, 65, 11, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 276 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086908 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086908 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086908/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086908 Building REAL300000086909 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086909' /scratch/stefan/7769667/working/building/REAL300000086909 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086909 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086909/0 /scratch/stefan/7769667/working/building/REAL300000086909 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/948 `/scratch/stefan/7769667/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(OC)=C1O) `REAL300000086909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086909 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(OC)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 328 conformations in input total number of sets (complete confs): 328 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 12, 12, 63, 156, 156, 155, 155, 156, 156, 156, 156, 1, 1, 1, 3, 1, 1, 4, 4, 4, 1, 12, 63, 156, 156, 156, 1, 4, 4, 4, 2] 328 rigid atoms, others: [32, 1, 2, 3, 4, 5, 17, 18, 19, 21, 22, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086909 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(OC)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 282 conformations in input total number of sets (complete confs): 282 using faster count positions algorithm for large data unique positions, atoms: [141, 118, 118, 118, 71, 71, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 141, 118, 118, 141, 141, 141, 118, 71, 13, 1, 1, 1, 118, 141, 141, 141, 236] 282 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 500 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086909 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086909 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086909/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086909 Building REAL300000086910 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086910' /scratch/stefan/7769667/working/building/REAL300000086910 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086910 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086910/0 /scratch/stefan/7769667/working/building/REAL300000086910 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/949 `/scratch/stefan/7769667/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(C(F)(F)F)=C1) `REAL300000086910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086910 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [68, 69, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 135, 135, 135, 135, 135, 135, 135, 135, 135, 69, 69, 69, 13, 1, 1, 1, 135, 135, 135, 135] 135 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 1, 2, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086910 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 45, 135, 135, 135, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 11, 11, 11, 45, 135, 135, 135, 1, 1, 1, 1] 135 rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 243 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086910 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086910 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086910/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086910 Building REAL300000086911 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086911' /scratch/stefan/7769667/working/building/REAL300000086911 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086911 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086911/0 /scratch/stefan/7769667/working/building/REAL300000086911 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/950 `/scratch/stefan/7769667/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC(Cl)=CC=C1Cl) `REAL300000086911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086911 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC(Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 78, 78, 78, 78, 78, 78, 78, 51, 51, 51, 11, 1, 1, 1, 78, 78, 78] 78 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086911 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC(Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 31, 78, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 31, 78, 78, 78, 1, 1, 1] 78 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 152 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086911 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086911 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086911/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086911 Building REAL300000086912 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086912' /scratch/stefan/7769667/working/building/REAL300000086912 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086912 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086912/0 /scratch/stefan/7769667/working/building/REAL300000086912 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/951 `/scratch/stefan/7769667/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C=C1Cl) `REAL300000086912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086912 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [50, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 69, 69, 51, 69, 69, 69, 69, 51, 51, 51, 11, 1, 1, 1, 69, 69, 69] 69 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086912 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 29, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 29, 69, 69, 69, 1, 1, 1] 69 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 133 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086912 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086912 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086912/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086912 Building REAL300000086913 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086913' /scratch/stefan/7769667/working/building/REAL300000086913 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086913 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086913/0 /scratch/stefan/7769667/working/building/REAL300000086913 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/952 `/scratch/stefan/7769667/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1O) `REAL300000086913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086913 none CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 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: [38, 10, 1, 1, 1, 1, 1, 7, 7, 40, 126, 127, 127, 127, 127, 127, 127, 127, 1, 1, 1, 1, 38, 38, 38, 38, 38, 1, 7, 40, 127, 127, 127, 1, 1, 2] 402 rigid atoms, others: [33, 2, 3, 4, 5, 6, 34, 18, 19, 20, 21, 27] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 35]) total number of confs: 337 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086913 none CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 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: [201, 194, 127, 127, 127, 51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 201, 201, 201, 201, 201, 127, 51, 11, 1, 1, 1, 127, 127, 254] 402 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 610 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086913 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086913 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086913/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086913 Building REAL300000086914 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086914' /scratch/stefan/7769667/working/building/REAL300000086914 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086914 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086914/0 /scratch/stefan/7769667/working/building/REAL300000086914 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/953 `/scratch/stefan/7769667/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(Cl)C=CC=C2Cl)C=N1) `REAL300000086914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086914 none O=C([O-])C1=CC=C(NN=CC2=C(Cl)C=CC=C2Cl)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 16, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 35, 35, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 12, 35, 52, 52, 52, 1] 52 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086914 none O=C([O-])C1=CC=C(NN=CC2=C(Cl)C=CC=C2Cl)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 16, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 52, 52, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 26, 6, 1, 1, 1, 52] 52 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086914 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086914 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086914/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086914 Building REAL300000086915 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086915' /scratch/stefan/7769667/working/building/REAL300000086915 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086915 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086915/0 /scratch/stefan/7769667/working/building/REAL300000086915 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/954 `/scratch/stefan/7769667/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C2SC3=CC=CC=C3NC2=C1) `REAL300000086915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086915 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C2SC3=CC=CC=C3NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [54, 55, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 55, 55, 55, 12, 1, 1, 1, 117, 117, 117, 117, 117, 117, 117, 117] 117 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 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: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086915 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C2SC3=CC=CC=C3NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 52, 117, 117, 117, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 52, 117, 117, 117, 1, 1, 1, 1, 1, 1, 1, 1] 117 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 33, 27, 28, 29, 30, 31]) total number of confs: 222 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086915 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086915 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086915/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086915 Building REAL300000086916 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086916' /scratch/stefan/7769667/working/building/REAL300000086916 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086916 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086916/0 /scratch/stefan/7769667/working/building/REAL300000086916 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/955 `/scratch/stefan/7769667/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(OC)C=C1C=NNC1=CC=C(C(=O)[O-])N=C1) `REAL300000086916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086916 none COC1=CC(OC)=C(OC)C=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 3, 1, 1, 3, 1, 1, 1, 8, 8, 38, 111, 111, 111, 111, 111, 111, 111, 111, 3, 3, 3, 1, 4, 4, 4, 4, 4, 4, 1, 8, 38, 111, 111, 111] 201 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 10, 11, 12, 34, 27] set([0, 6, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086916 none COC1=CC(OC)=C(OC)C=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [157, 111, 111, 111, 111, 111, 182, 111, 111, 176, 111, 51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 157, 157, 157, 111, 182, 182, 182, 176, 176, 176, 111, 51, 11, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 505 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086916 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086916 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086916/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086916 Building REAL300000086917 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086917' /scratch/stefan/7769667/working/building/REAL300000086917 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086917 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086917/0 /scratch/stefan/7769667/working/building/REAL300000086917 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/956 `/scratch/stefan/7769667/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C2O1) `REAL300000086917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086917 none CCCCC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7] 0 hydrogens 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, 9, 5, 1, 1, 1, 1, 6, 6, 31, 76, 76, 75, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 15, 15, 9, 9, 5, 5, 6, 31, 76, 76, 76, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 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]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086917 none CCCCC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 175, 76, 76, 29, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 76, 76, 201, 201, 201, 201, 201, 201, 201, 175, 175, 29, 7, 1, 1, 1, 76, 76, 76, 76] 201 rigid atoms, others: [36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 711 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086917 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086917 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086917/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086917 Building REAL300000086918 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086918' /scratch/stefan/7769667/working/building/REAL300000086918 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086918 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086918/0 /scratch/stefan/7769667/working/building/REAL300000086918 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/957 `/scratch/stefan/7769667/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2CC(C3=CC=CC=C3)OC3=CC=CC=C32)C=N1) `REAL300000086918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086918 none O=C([O-])C1=CC=C(NN=C2CC(C3=CC=CC=C3)OC3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 10, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 10, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1] 57 rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 82 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: REAL300000086918 none O=C([O-])C1=CC=C(NN=C2CC(C3=CC=CC=C3)OC3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 57, 19, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 57, 57, 57, 57, 19, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 57] 57 rigid atoms, others: [33, 34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42]) total number of confs: 98 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086918 none O=C([O-])C1=CC=C(NN=C2CC(C3=CC=CC=C3)OC3=CC=CC=C32)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 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] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 57, 10, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 10, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 57] 57 rigid atoms, others: [32, 41, 38, 7, 8, 9, 10, 11, 12, 40, 18, 19, 20, 21, 22, 23, 24, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 42]) total number of confs: 81 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086918 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086918 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086918/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086918 Building REAL300000086919 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086919' /scratch/stefan/7769667/working/building/REAL300000086919 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086919 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086919/0 /scratch/stefan/7769667/working/building/REAL300000086919 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/958 `/scratch/stefan/7769667/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC)C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=C1) `REAL300000086919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086919 none COC1=CC=C(OC)C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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, 12, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 12, 12, 12, 58, 179, 179, 179, 179, 179, 179, 179, 179, 1, 3, 3, 3, 1, 1, 3, 3, 3, 13, 13, 13, 58, 179, 179, 179, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 8, 9, 38, 22, 26, 27] set([0, 7, 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]) total number of confs: 324 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086919 none COC1=CC=C(OC)C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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, 12, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 179, 179, 179, 179, 179, 179, 199, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 179, 201, 201, 201, 179, 179, 199, 199, 199, 50, 50, 50, 11, 1, 1, 1, 179] 201 rigid atoms, others: [35, 36, 37, 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, 33, 34, 38]) total number of confs: 320 number of broken/clashed sets: 80 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086919 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086919 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086919/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086919 Building REAL300000086920 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086920' /scratch/stefan/7769667/working/building/REAL300000086920 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086920 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086920/0 /scratch/stefan/7769667/working/building/REAL300000086920 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/959 `/scratch/stefan/7769667/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1OC(C)C) `REAL300000086920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086920 none COC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 22, 91, 91, 91, 91, 91, 91, 91, 91, 1, 1, 7, 17, 17, 4, 4, 4, 1, 1, 1, 4, 22, 91, 91, 91, 17, 17, 17, 17, 17, 17, 17] 142 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 20, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086920 none COC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [136, 91, 91, 91, 91, 91, 52, 52, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 91, 91, 141, 142, 142, 136, 136, 136, 91, 91, 91, 52, 11, 1, 1, 1, 142, 142, 142, 142, 142, 142, 142] 142 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086920 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086920 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086920/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086920 Building REAL300000086921 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086921' /scratch/stefan/7769667/working/building/REAL300000086921 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086921 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086921/0 /scratch/stefan/7769667/working/building/REAL300000086921 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/960 `/scratch/stefan/7769667/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OC) `REAL300000086921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086921 none CCNC(=O)COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens 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, 43, 43, 27, 43, 9, 1, 1, 1, 1, 1, 1, 6, 6, 10, 21, 21, 20, 21, 21, 21, 21, 21, 1, 1, 1, 3, 77, 77, 77, 77, 77, 43, 27, 27, 1, 1, 6, 10, 21, 21, 21, 1, 3, 3, 3] 201 rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 23, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086921 none CCNC(=O)COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 159, 159, 142, 159, 81, 21, 21, 21, 21, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 36, 201, 201, 201, 201, 201, 159, 142, 142, 21, 21, 7, 3, 1, 1, 1, 21, 36, 36, 36] 201 rigid atoms, others: [39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 747 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086921 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086921 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086921/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086921 Building REAL300000086922 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086922' /scratch/stefan/7769667/working/building/REAL300000086922 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086922 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086922/0 /scratch/stefan/7769667/working/building/REAL300000086922 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/961 `/scratch/stefan/7769667/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=CC=C1OCC) `REAL300000086922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086922 none CCCOC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=CC=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7] 0 hydrogens 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, 13, 3, 1, 1, 1, 1, 4, 4, 10, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 10, 36, 27, 27, 27, 27, 27, 13, 13, 4, 10, 34, 34, 34, 1, 1, 1, 36, 36, 36, 36, 36] 201 rigid atoms, others: [3, 4, 5, 6, 39, 18, 19, 20, 21, 22, 38, 37] set([0, 1, 2, 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, 40, 41, 42, 43, 44]) total number of confs: 305 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086922 none CCCOC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=CC=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7] 0 hydrogens 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, 108, 45, 34, 34, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 116, 177, 161, 161, 161, 161, 161, 108, 108, 19, 7, 1, 1, 1, 34, 34, 34, 177, 177, 177, 177, 177] 201 rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 1098 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086922 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086922 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086922/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086922 Building REAL300000086923 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086923' /scratch/stefan/7769667/working/building/REAL300000086923 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086923 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086923/0 /scratch/stefan/7769667/working/building/REAL300000086923 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/962 `/scratch/stefan/7769667/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1) `REAL300000086923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086923 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [46, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 96, 96, 54, 55, 147, 146, 146, 144, 144, 145, 147, 96, 96, 47, 47, 47, 11, 1, 1, 1, 96, 96, 147, 144, 96, 96] 147 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 388 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: REAL300000086923 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 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: [26, 2, 26, 26, 91, 147, 147, 147, 147, 147, 147, 147, 147, 2, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 26, 26, 26, 91, 147, 147, 147, 12, 12, 1, 1, 12, 12] 147 rigid atoms, others: [36, 37, 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, 38, 39]) total number of confs: 351 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086923 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 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: [6, 1, 6, 6, 33, 96, 96, 96, 96, 96, 96, 96, 96, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 6, 6, 6, 33, 96, 96, 96, 1, 1, 12, 12, 1, 1] 147 rigid atoms, others: [1, 34, 35, 38, 39, 13, 14, 15, 16, 17, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 174 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086923 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086923 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086923/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086923 Building REAL300000086924 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086924' /scratch/stefan/7769667/working/building/REAL300000086924 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086924 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086924/0 /scratch/stefan/7769667/working/building/REAL300000086924 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/963 `/scratch/stefan/7769667/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC) `REAL300000086924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086924 none CCCCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 51, 26, 10, 1, 1, 1, 1, 1, 7, 7, 12, 22, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 3, 53, 53, 53, 53, 53, 53, 53, 26, 26, 1, 7, 12, 23, 23, 23, 1, 1, 4, 4, 4] 201 rigid atoms, others: [34, 4, 5, 6, 7, 8, 41, 40, 20, 21, 22, 23] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086924 none CCCCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 134, 80, 23, 23, 23, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 39, 201, 201, 201, 201, 201, 201, 201, 134, 134, 23, 9, 5, 1, 1, 1, 23, 23, 39, 39, 39] 201 rigid atoms, others: [37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 735 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086924 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086924 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086924/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086924 Building REAL300000086925 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086925' /scratch/stefan/7769667/working/building/REAL300000086925 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086925 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086925/0 /scratch/stefan/7769667/working/building/REAL300000086925 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/964 `/scratch/stefan/7769667/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C(OCCC)=C1) `REAL300000086925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086925 none CCCOC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 5, 5, 5, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [15, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 6, 14, 28, 1, 15, 15, 15, 15, 15, 7, 7, 1, 1, 5, 5, 5, 13, 21, 21, 21, 14, 14, 29, 29, 29, 29, 29, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 50, 35, 21, 22, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086925 none CCCOC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 12, 5, 5, 5, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [152, 71, 71, 21, 19, 21, 21, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 35, 67, 95, 21, 152, 152, 152, 152, 152, 71, 71, 21, 21, 11, 11, 11, 3, 1, 1, 1, 67, 67, 96, 96, 96, 96, 96, 21] 201 rigid atoms, others: [40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 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: 858 number of broken/clashed sets: 90 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086925 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086925 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086925/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086925 Building REAL300000086926 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086926' /scratch/stefan/7769667/working/building/REAL300000086926 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086926 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086926/0 /scratch/stefan/7769667/working/building/REAL300000086926 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/965 `/scratch/stefan/7769667/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC(=O)[O-]) `REAL300000086926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086926 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 17, 54, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 9, 37, 63, 63, 4, 4, 4, 1, 7, 17, 55, 55, 55, 1, 1, 37, 37] 201 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 17, 18, 19, 20, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086926 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 55, 55, 55, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 147, 201, 201, 201, 87, 87, 87, 55, 23, 7, 1, 1, 1, 55, 55, 201, 201] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 545 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086926 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086926 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086926/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086926 Building REAL300000086927 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086927' /scratch/stefan/7769667/working/building/REAL300000086927 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086927 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086927/0 /scratch/stefan/7769667/working/building/REAL300000086927 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/966 `/scratch/stefan/7769667/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=C(C)C2=CC=CC=C2O1) `REAL300000086927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086927 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=C(C)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [44, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 65, 65, 65, 65, 65, 65, 65, 65, 65, 45, 45, 45, 11, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65] 65 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086927 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=C(C)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 24, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 23, 65, 65, 65, 2, 2, 2, 1, 1, 1, 1] 65 rigid atoms, others: [1, 34, 35, 36, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 138 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086927 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086927 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086927/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086927 Building REAL300000086928 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086928' /scratch/stefan/7769667/working/building/REAL300000086928 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086928 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086928/0 /scratch/stefan/7769667/working/building/REAL300000086928 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/967 `/scratch/stefan/7769667/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC(C)=CC=C2C)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1) `REAL300000086928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086928 none CC1=NN(C2=CC(C)=CC=C2C)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 8, 1, 1, 1, 5, 1, 1, 1, 5, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 10, 10, 46, 107, 107, 107, 107, 107, 107, 107, 107, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 45, 107, 107, 107] 167 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086928 none CC1=NN(C2=CC(C)=CC=C2C)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 8, 1, 1, 1, 5, 1, 1, 1, 5, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 167, 167, 167, 167, 167, 167, 167, 107, 107, 57, 57, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 167, 167, 167, 167, 167, 167, 167, 167, 167, 57, 13, 1, 1, 1] 167 rigid atoms, others: [41, 42, 43, 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, 37, 38, 39, 40]) total number of confs: 272 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086928 none CC1=NN(C2=CC(C)=CC=C2C)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 8, 1, 1, 1, 5, 1, 1, 1, 5, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 39, 39, 97, 167, 167, 167, 167, 167, 167, 167, 167, 7, 7, 7, 1, 2, 2, 2, 1, 1, 2, 2, 2, 39, 97, 167, 167, 167] 167 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 386 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086928 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086928 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086928/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086928 Building REAL300000086929 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086929' /scratch/stefan/7769667/working/building/REAL300000086929 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086929 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086929/0 /scratch/stefan/7769667/working/building/REAL300000086929 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/968 `/scratch/stefan/7769667/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC1CCCO1) `REAL300000086929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086929 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 5, 5, 5, 5, 5, 12, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 1, 7, 7, 38, 104, 104, 104, 104, 104, 104, 104, 104, 1, 1, 1, 1, 2, 9, 9, 9, 9, 2, 2, 2, 1, 7, 38, 104, 104, 104, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086929 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 5, 5, 5, 5, 5, 12, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [9, 9, 9, 9, 9, 31, 31, 108, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 31, 108, 201, 201, 201, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 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]) total number of confs: 438 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086929 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 5, 5, 5, 5, 5, 12, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [104, 104, 104, 55, 55, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 141, 201, 201, 201, 201, 104, 104, 104, 104, 55, 12, 1, 1, 1, 104, 104, 104, 141, 141, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 620 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086929 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086929/1 /scratch/stefan/7769667/working/building/REAL300000086929 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/969 `/scratch/stefan/7769667/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC1CCCO1) `REAL300000086929.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086929/1/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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086929 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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, 1, 8, 31, 32, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 2, 5, 5, 5, 5, 2, 2, 2, 1, 8, 8, 59, 59, 59, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086929 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [5, 5, 5, 5, 5, 29, 104, 104, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 29, 29, 201, 201, 201, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 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]) total number of confs: 393 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086929 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [59, 59, 59, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 113, 201, 201, 201, 201, 59, 59, 59, 59, 21, 22, 1, 1, 1, 59, 59, 59, 113, 113, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 794 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086929 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086929 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086929/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086929/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086929 Building REAL300000086930 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086930' /scratch/stefan/7769667/working/building/REAL300000086930 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086930 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086930/0 /scratch/stefan/7769667/working/building/REAL300000086930 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/970 `/scratch/stefan/7769667/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C1=NN(C2=CC=CC=C2)C=C1C=NNC1=CC=C(C(=O)[O-])N=C1) `REAL300000086930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086930 none CC1=CC=CC=C1C1=NN(C2=CC=CC=C2)C=C1C=NNC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 167, 167, 111, 111, 111, 111, 111, 114, 114, 111, 114, 114, 111, 58, 58, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 167, 167, 167, 114, 114, 111, 114, 114, 111, 58, 11, 1, 1, 1] 167 rigid atoms, others: [45, 46, 47, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 284 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086930 none CC1=CC=CC=C1C1=NN(C2=CC=CC=C2)C=C1C=NNC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 17, 17, 9, 17, 17, 9, 9, 9, 28, 28, 87, 167, 167, 167, 167, 167, 167, 167, 167, 2, 2, 2, 1, 1, 1, 1, 17, 17, 9, 17, 17, 9, 28, 87, 167, 167, 167] 167 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 394 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086930 none CC1=CC=CC=C1C1=NN(C2=CC=CC=C2)C=C1C=NNC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 18, 18, 47, 114, 114, 114, 114, 114, 114, 114, 114, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 4, 18, 47, 114, 114, 114] 167 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086930 none CC1=CC=CC=C1C1=NN(C2=CC=CC=C2)C=C1C=NNC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 11, 11, 41, 111, 111, 111, 111, 111, 111, 111, 111, 9, 9, 9, 9, 9, 9, 9, 4, 4, 1, 4, 4, 1, 11, 41, 111, 111, 111] 167 rigid atoms, others: [6, 7, 8, 9, 10, 16, 17, 18, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 19, 20, 21, 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: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086930 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086930 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086930/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086930 Building REAL300000086931 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086931' /scratch/stefan/7769667/working/building/REAL300000086931 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086931 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086931/0 /scratch/stefan/7769667/working/building/REAL300000086931 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/971 `/scratch/stefan/7769667/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(O)=C1O) `REAL300000086931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086931 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(O)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 26, 67, 67, 66, 66, 67, 67, 67, 67, 1, 1, 1, 1, 1, 4, 4, 4, 1, 6, 26, 67, 67, 67, 1, 2, 2] 268 rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 148 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086931 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(O)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 37, 37, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 38, 61, 67, 67, 67, 67, 37, 11, 1, 1, 1, 67, 134, 134] 268 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 33, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 500 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086931 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086931 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086931/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086931 Building REAL300000086932 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086932' /scratch/stefan/7769667/working/building/REAL300000086932 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086932 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086932/0 /scratch/stefan/7769667/working/building/REAL300000086932 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/972 `/scratch/stefan/7769667/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OC(C)C)C=C1) `REAL300000086932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086932 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 127, 127, 49, 86, 201, 201, 201, 127, 127, 49, 49, 49, 11, 1, 1, 1, 127, 127, 201, 201, 201, 201, 201, 201, 201, 127, 127] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 1, 2, 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: 597 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086932 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 31, 127, 127, 127, 127, 127, 127, 127, 127, 1, 1, 1, 1, 1, 12, 26, 26, 1, 1, 6, 6, 6, 31, 127, 127, 127, 1, 1, 26, 26, 26, 26, 26, 26, 26, 1, 1] 201 rigid atoms, others: [1, 39, 40, 13, 14, 15, 16, 17, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 277 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086932 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086932 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086932/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086932 Building REAL300000086933 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086933' /scratch/stefan/7769667/working/building/REAL300000086933 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086933 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086933/0 /scratch/stefan/7769667/working/building/REAL300000086933 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/973 `/scratch/stefan/7769667/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC2=NC(C)=C(C=NNC3=CC=C(C(=O)[O-])N=C3)N12) `REAL300000086933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086933 none CC1=CSC2=NC(C)=C(C=NNC3=CC=C(C(=O)[O-])N=C3)N12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 56, 105, 105, 105, 105, 105, 105, 105, 105, 1, 2, 2, 2, 1, 2, 2, 2, 12, 56, 105, 105, 105] 105 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 25] set([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: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086933 none CC1=CSC2=NC(C)=C(C=NNC3=CC=C(C(=O)[O-])N=C3)N12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 105, 105, 105, 105, 60, 60, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 105, 105, 105, 60, 13, 1, 1, 1] 105 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086933 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086933 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086933/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086933 Building REAL300000086934 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086934' /scratch/stefan/7769667/working/building/REAL300000086934 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086934 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086934/0 /scratch/stefan/7769667/working/building/REAL300000086934 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/974 `/scratch/stefan/7769667/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OC(F)F) `REAL300000086934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086934 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OC(F)F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [3, 1, 1, 1, 1, 1, 1, 6, 6, 22, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 9, 46, 46, 4, 4, 4, 1, 1, 6, 22, 68, 68, 68, 1, 46] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 18, 19, 20, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 35]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086934 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OC(F)F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [123, 68, 68, 68, 68, 29, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 156, 200, 200, 123, 123, 123, 68, 68, 29, 7, 1, 1, 1, 68, 201] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 594 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086934 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086934 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086934/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086934 Building REAL300000086935 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086935' /scratch/stefan/7769667/working/building/REAL300000086935 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086935 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086935/0 /scratch/stefan/7769667/working/building/REAL300000086935 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/975 `/scratch/stefan/7769667/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(OC)=C1) `REAL300000086935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086935 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 6, 6, 30, 95, 95, 94, 94, 95, 95, 95, 95, 1, 1, 1, 2, 1, 2, 2, 2, 1, 6, 30, 95, 95, 95, 1, 3, 3, 3, 1] 132 rigid atoms, others: [1, 2, 3, 4, 5, 35, 17, 18, 19, 21, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086935 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [116, 95, 95, 95, 70, 70, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 117, 95, 116, 116, 116, 95, 70, 13, 1, 1, 1, 95, 117, 117, 117, 95] 132 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086935 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086935 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086935/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086935 Building REAL300000086936 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086936' /scratch/stefan/7769667/working/building/REAL300000086936 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086936 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086936/0 /scratch/stefan/7769667/working/building/REAL300000086936 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/976 `/scratch/stefan/7769667/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(I)C=C1) `REAL300000086936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086936 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(I)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [38, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 48, 48, 39, 48, 48, 48, 39, 39, 39, 11, 1, 1, 1, 48, 48, 48, 48] 48 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086936 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(I)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 16, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 48, 48, 48, 1, 1, 1, 1] 48 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 86 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086936 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086936 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086936/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086936 Building REAL300000086937 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086937' /scratch/stefan/7769667/working/building/REAL300000086937 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086937 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086937/0 /scratch/stefan/7769667/working/building/REAL300000086937 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/977 `/scratch/stefan/7769667/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=CC=C(C=NNC3=CC=C(C(=O)[O-])N=C3)C=C2C=C1) `REAL300000086937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086937 none COC1=CC2=CC=C(C=NNC3=CC=C(C(=O)[O-])N=C3)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 54, 127, 127, 126, 126, 127, 127, 127, 127, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 10, 54, 127, 127, 127, 1, 1, 1] 127 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 35, 20, 21, 22, 23, 36, 27, 28, 29, 37] set([0, 32, 34, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 30, 31]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086937 none COC1=CC2=CC=C(C=NNC3=CC=C(C(=O)[O-])N=C3)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 127, 127, 127, 53, 53, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 53, 13, 1, 1, 1, 127, 127, 127] 127 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 187 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086937 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086937 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086937/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086937 Building REAL300000086938 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086938' /scratch/stefan/7769667/working/building/REAL300000086938 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086938 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086938/0 /scratch/stefan/7769667/working/building/REAL300000086938 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/978 `/scratch/stefan/7769667/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1O) `REAL300000086938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086938 none COC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 13, 13, 13, 76, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 3, 3, 3, 1, 13, 13, 13, 76, 201, 201, 201, 1, 1, 2] 402 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 18, 19, 20, 21, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 359 number of broken/clashed sets: 154 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086938 none COC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 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: [201, 201, 201, 201, 68, 68, 68, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 68, 68, 68, 13, 1, 1, 1, 201, 201, 402] 402 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 685 number of broken/clashed sets: 154 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086938 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086938 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086938/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086938 Building REAL300000086939 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086939' /scratch/stefan/7769667/working/building/REAL300000086939 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086939 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086939/0 /scratch/stefan/7769667/working/building/REAL300000086939 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/979 `/scratch/stefan/7769667/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC([N+](=O)[O-])=CC=C2[O-])C=N1) `REAL300000086939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086939 none O=C([O-])C1=CC=C(NN=CC2=CC([N+](=O)[O-])=CC=C2[O-])C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 12, 18, 19, 19, 19, 1] 19 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086939 none O=C([O-])C1=CC=C(NN=CC2=CC([N+](=O)[O-])=CC=C2[O-])C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 3, 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, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 8, 4, 1, 1, 1, 19] 19 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086939 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086939 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086939/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086939 Building REAL300000086940 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086940' /scratch/stefan/7769667/working/building/REAL300000086940 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086940 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086940/0 /scratch/stefan/7769667/working/building/REAL300000086940 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/980 `/scratch/stefan/7769667/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CS2)C=N1) `REAL300000086940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086940 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CS2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 14, 1, 8, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 10, 39, 39, 54, 54, 54, 54, 54, 1, 1, 1, 1, 10, 39, 54, 54, 1] 54 rigid atoms, others: [1, 3, 4, 5, 6, 7, 16, 17, 18, 19, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086940 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CS2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 14, 1, 8, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 54, 54, 25, 9, 9, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 25, 9, 1, 1, 54] 54 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086940 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086940 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086940/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086940 Building REAL300000086941 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086941' /scratch/stefan/7769667/working/building/REAL300000086941 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086941 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086941/0 /scratch/stefan/7769667/working/building/REAL300000086941 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/981 `/scratch/stefan/7769667/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1) `REAL300000086941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086941 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [28, 13, 28, 3, 1, 1, 1, 1, 1, 1, 8, 8, 44, 117, 117, 116, 117, 117, 117, 117, 117, 1, 1, 13, 13, 1, 1, 8, 44, 117, 117, 117, 1, 1] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 21, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 299 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086941 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 161, 89, 58, 117, 117, 58, 58, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 117, 117, 58, 11, 1, 1, 1, 117, 117] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 695 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086941 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086941 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086941/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086941 Building REAL300000086942 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086942' /scratch/stefan/7769667/working/building/REAL300000086942 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086942 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086942/0 /scratch/stefan/7769667/working/building/REAL300000086942 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/982 `/scratch/stefan/7769667/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(OCC(=O)[O-])=C1) `REAL300000086942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086942 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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] 0 hydrogens 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, 33, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 76, 76, 76, 76, 76, 162, 201, 201, 201, 76, 33, 33, 33, 7, 1, 1, 1, 76, 76, 76, 201, 201, 76] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 462 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086942 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 25, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 6, 20, 37, 37, 1, 9, 9, 9, 25, 76, 76, 76, 1, 1, 1, 20, 20, 1] 201 rigid atoms, others: [32, 1, 36, 33, 13, 14, 15, 16, 17, 18, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 244 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086942 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086942 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086942/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086942 Building REAL300000086943 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086943' /scratch/stefan/7769667/working/building/REAL300000086943 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086943 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086943/0 /scratch/stefan/7769667/working/building/REAL300000086943 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/983 `/scratch/stefan/7769667/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OCC) `REAL300000086943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086943 none CCCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7] 0 hydrogens 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, 31, 9, 1, 1, 1, 1, 1, 1, 4, 4, 8, 15, 15, 14, 14, 15, 15, 15, 15, 1, 1, 1, 9, 15, 60, 59, 59, 60, 60, 59, 59, 31, 31, 1, 1, 4, 8, 15, 15, 15, 1, 15, 15, 16, 16, 16] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 42, 21, 22, 23, 36] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086943 none CCCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 129, 67, 15, 15, 15, 15, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 60, 74, 173, 173, 173, 173, 173, 173, 173, 129, 129, 15, 15, 7, 3, 1, 1, 1, 15, 74, 74, 74, 74, 74] 201 rigid atoms, others: [39, 40, 41, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47]) total number of confs: 741 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086943 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086943 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086943/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086943 Building REAL300000086944 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086944' /scratch/stefan/7769667/working/building/REAL300000086944 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086944 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086944/0 /scratch/stefan/7769667/working/building/REAL300000086944 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/984 `/scratch/stefan/7769667/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2)C(C)=C1C=NNC1=CC=C(C(=O)[O-])N=C1) `REAL300000086944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086944 none CC1=NN(C2=CC=CC=C2)C(C)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 1, 1, 1, 12, 12, 74, 190, 190, 190, 190, 190, 190, 190, 190, 2, 2, 2, 5, 5, 1, 5, 5, 2, 2, 2, 12, 74, 190, 190, 190] 193 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]) total number of confs: 368 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086944 none CC1=NN(C2=CC=CC=C2)C(C)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 190, 190, 190, 193, 193, 190, 193, 193, 190, 190, 72, 72, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 190, 190, 190, 193, 193, 190, 193, 193, 190, 190, 190, 72, 13, 1, 1, 1] 193 rigid atoms, others: [38, 39, 40, 15, 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, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 281 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086944 none CC1=NN(C2=CC=CC=C2)C(C)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 31, 31, 103, 193, 193, 193, 193, 193, 193, 193, 193, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 31, 103, 193, 193, 193] 193 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 412 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086944 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086944 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086944/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086944 Building REAL300000086945 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086945' /scratch/stefan/7769667/working/building/REAL300000086945 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086945 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086945/0 /scratch/stefan/7769667/working/building/REAL300000086945 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/985 `/scratch/stefan/7769667/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=C(C2=CC=CC=C2)C=C1)N=NC1=CC=C(C(=O)[O-])N=C1) `REAL300000086945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086945 none CC(CC1=CC=C(C2=CC=CC=C2)C=C1)N=NC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [9, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 10, 55, 55, 125, 125, 125, 125, 125, 125, 125, 125, 10, 10, 10, 10, 3, 3, 1, 1, 3, 3, 2, 3, 3, 1, 1, 125, 125, 125] 125 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 13, 14] set([0, 1, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 226 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: REAL300000086945 none CC(CC1=CC=C(C2=CC=CC=C2)C=C1)N=NC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [47, 9, 47, 106, 125, 125, 122, 114, 125, 125, 125, 125, 125, 125, 125, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 106, 106, 125, 125, 125, 125, 125, 125, 125, 125, 125, 1, 1, 1] 125 rigid atoms, others: [41, 42, 43, 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, 38, 39, 40]) total number of confs: 474 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086945 none CC(CC1=CC=C(C2=CC=CC=C2)C=C1)N=NC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [16, 7, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 64, 64, 125, 125, 125, 125, 125, 125, 125, 125, 17, 17, 17, 17, 7, 7, 3, 3, 1, 1, 1, 1, 1, 3, 3, 125, 125, 125] 125 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 34, 35, 38] 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, 33, 39, 40, 41, 42, 43]) total number of confs: 253 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086945 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086945 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086945/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086945 Building REAL300000086946 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086946' /scratch/stefan/7769667/working/building/REAL300000086946 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086946 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086946/0 /scratch/stefan/7769667/working/building/REAL300000086946 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/986 `/scratch/stefan/7769667/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC([N+](=O)[O-])=C1) `REAL300000086946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086946 none CCCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 98, 38, 39, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 172, 172, 39, 172, 172, 172, 172, 172, 108, 108, 108, 108, 108, 98, 98, 7, 1, 1, 1, 172, 172, 55, 172] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 805 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086946 none CCCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 35, 12, 1, 12, 12, 66, 172, 172, 171, 172, 172, 172, 172, 172, 1, 1, 1, 1, 1, 1, 2, 2, 1, 45, 45, 45, 45, 45, 35, 35, 66, 172, 172, 172, 1, 1, 1, 1] 201 rigid atoms, others: [19, 3, 36, 37, 38, 15, 16, 17, 18, 35, 20, 23] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 490 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086946 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086946 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086946/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086946 Building REAL300000086947 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086947' /scratch/stefan/7769667/working/building/REAL300000086947 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086947 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086947/0 /scratch/stefan/7769667/working/building/REAL300000086947 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/987 `/scratch/stefan/7769667/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1OC(F)F) `REAL300000086947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086947 none COC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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, 11, 11, 8, 1, 1, 12, 5, 15, 15, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 22, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1, 6, 34, 34, 4, 4, 4, 1, 1, 1, 4, 22, 81, 81, 81, 34] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 20, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086947 none COC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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, 11, 11, 8, 1, 1, 12, 5, 15, 15, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [143, 81, 81, 81, 81, 81, 53, 53, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 149, 201, 201, 143, 143, 143, 81, 81, 81, 53, 12, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 637 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086947 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086947 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086947/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086947 Building REAL300000086948 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086948' /scratch/stefan/7769667/working/building/REAL300000086948 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086948 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086948/0 /scratch/stefan/7769667/working/building/REAL300000086948 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/988 `/scratch/stefan/7769667/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(C3=CC=CC=C3)N=C3SC=CN23)C=N1) `REAL300000086948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086948 none O=C([O-])C1=CC=C(NN=CC2=C(C3=CC=CC=C3)N=C3SC=CN23)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 14, 1, 1, 8, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 13, 68, 68, 121, 121, 123, 123, 121, 123, 123, 121, 121, 121, 121, 121, 121, 1, 1, 1, 1, 13, 68, 123, 123, 121, 123, 123, 121, 121, 1] 123 rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26, 27, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086948 none O=C([O-])C1=CC=C(NN=CC2=C(C3=CC=CC=C3)N=C3SC=CN23)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 14, 1, 1, 8, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 123, 123, 123, 67, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 123, 123, 123, 123, 67, 16, 1, 1, 1, 1, 1, 6, 6, 123] 123 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 265 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086948 none O=C([O-])C1=CC=C(NN=CC2=C(C3=CC=CC=C3)N=C3SC=CN23)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 14, 1, 1, 8, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 121, 121, 121, 43, 7, 7, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 43, 7, 6, 6, 1, 6, 6, 1, 1, 121] 123 rigid atoms, others: [35, 36, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37]) total number of confs: 227 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086948 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086948 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086948/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086948 Building REAL300000086949 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086949' /scratch/stefan/7769667/working/building/REAL300000086949 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086949 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086949/0 /scratch/stefan/7769667/working/building/REAL300000086949 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/989 `/scratch/stefan/7769667/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C(Cl)=C1Cl) `REAL300000086949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086949 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 16, 1, 16, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [47, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 70, 70, 70, 70, 70, 70, 70, 70, 47, 47, 47, 11, 1, 1, 1, 70, 70] 70 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086949 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(Cl)C(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 16, 1, 16, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [9, 1, 9, 9, 28, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 28, 70, 70, 70, 1, 1] 70 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 133 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086949 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086949 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086949/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086949 Building REAL300000086950 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086950' /scratch/stefan/7769667/working/building/REAL300000086950 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086950 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086950/0 /scratch/stefan/7769667/working/building/REAL300000086950 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/990 `/scratch/stefan/7769667/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(N2C=CN=C2)C=C1) `REAL300000086950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086950 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(N2C=CN=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [38, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 47, 47, 39, 39, 92, 92, 92, 92, 47, 47, 39, 39, 39, 11, 1, 1, 1, 47, 47, 92, 92, 92, 47, 47] 92 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 198 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: REAL300000086950 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(N2C=CN=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [11, 2, 10, 10, 33, 92, 92, 92, 92, 92, 92, 92, 92, 2, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 33, 92, 92, 92, 7, 7, 1, 1, 1, 7, 7] 92 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, 36, 37]) total number of confs: 193 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086950 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(N2C=CN=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 18, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 7, 6, 6, 7, 1, 1, 5, 5, 5, 18, 47, 47, 47, 1, 1, 7, 7, 7, 1, 1] 92 rigid atoms, others: [32, 1, 36, 37, 13, 14, 15, 16, 17, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 103 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086950 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086950 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086950/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086950 Building REAL300000086951 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086951' /scratch/stefan/7769667/working/building/REAL300000086951 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086951 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086951/0 /scratch/stefan/7769667/working/building/REAL300000086951 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/991 `/scratch/stefan/7769667/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OCC1=CC=CC=C1) `REAL300000086951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086951 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OCC1=CC=CC=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7] 0 hydrogens 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, 4, 4, 8, 19, 19, 18, 19, 19, 19, 19, 19, 1, 1, 1, 9, 39, 65, 65, 63, 65, 65, 4, 4, 4, 1, 1, 4, 8, 19, 19, 19, 1, 39, 39, 65, 65, 65, 65, 65] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 18, 19, 20, 38, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086951 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OCC1=CC=CC=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 65, 65, 65, 65, 65, 65, 94, 94, 125, 201, 201, 201, 201, 201, 201, 201, 201, 65, 17, 3, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 65, 65, 94, 125, 201, 201, 201, 65, 3, 3, 1, 1, 1, 1, 1] 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]) total number of confs: 484 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086951 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1OCC1=CC=CC=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 80, 178, 201, 201, 201, 201, 201, 37, 37, 37, 19, 19, 11, 7, 1, 1, 1, 19, 178, 178, 201, 201, 201, 201, 201] 201 rigid atoms, others: [35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 601 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086951 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086951 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086951/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086951 Building REAL300000086952 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086952' /scratch/stefan/7769667/working/building/REAL300000086952 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086952 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086952/0 /scratch/stefan/7769667/working/building/REAL300000086952 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/992 `/scratch/stefan/7769667/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(N2CCOCC2)C=C1) `REAL300000086952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086952 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(N2CCOCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [63, 64, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 64, 105, 105, 88, 105, 119, 119, 119, 119, 119, 105, 105, 64, 64, 64, 12, 1, 1, 1, 105, 105, 119, 119, 119, 119, 119, 119, 119, 119, 105, 105] 119 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 279 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: REAL300000086952 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(N2CCOCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [27, 5, 27, 27, 64, 119, 119, 119, 119, 119, 119, 119, 119, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 26, 27, 27, 64, 119, 119, 119, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 119 rigid atoms, others: [34, 35, 36, 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, 42, 43]) total number of confs: 282 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086952 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(N2CCOCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 35, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 7, 7, 7, 35, 105, 105, 105, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1] 119 rigid atoms, others: [32, 1, 33, 42, 43, 13, 14, 15, 16, 17, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 198 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086952 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086952 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086952/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086952 Building REAL300000086953 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086953' /scratch/stefan/7769667/working/building/REAL300000086953 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086953 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086953/0 /scratch/stefan/7769667/working/building/REAL300000086953 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/993 `/scratch/stefan/7769667/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(F)C=C3)O2)C=N1) `REAL300000086953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086953 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(F)C=C3)O2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 62, 62, 121, 121, 121, 121, 133, 133, 121, 121, 133, 133, 121, 1, 1, 1, 1, 12, 62, 121, 121, 133, 133, 133, 133, 1] 133 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086953 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(F)C=C3)O2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 133, 133, 133, 86, 32, 32, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 133, 133, 133, 133, 86, 32, 7, 7, 1, 1, 1, 1, 133] 133 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 302 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086953 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(F)C=C3)O2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 121, 121, 121, 46, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 7, 7, 1, 121, 121, 121, 121, 46, 8, 1, 1, 7, 7, 7, 7, 121] 133 rigid atoms, others: [9, 10, 11, 12, 13, 14, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086953 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086953 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086953/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086953 Building REAL300000086954 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086954' /scratch/stefan/7769667/working/building/REAL300000086954 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086954 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086954/0 /scratch/stefan/7769667/working/building/REAL300000086954 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/994 `/scratch/stefan/7769667/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C2OCOC2=C1)N=NC1=CC=C(C(=O)[O-])N=C1) `REAL300000086954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086954 none CC(CCC1=CC=C2OCOC2=C1)N=NC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 5, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 7, 7, 7, 3, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 118, 118, 201, 201, 201, 201, 201, 201, 201, 201, 41, 42, 42, 42, 10, 10, 6, 6, 1, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 35, 36] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086954 none CC(CCC1=CC=C2OCOC2=C1)N=NC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 5, 5, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 7, 7, 7, 3, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 9, 45, 95, 109, 201, 201, 201, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 100, 100, 109, 104, 201, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 590 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086954 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086954 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086954/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086954 Building REAL300000086955 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086955' /scratch/stefan/7769667/working/building/REAL300000086955 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086955 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086955/0 /scratch/stefan/7769667/working/building/REAL300000086955 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/995 `/scratch/stefan/7769667/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C2OCCOC2=C1) `REAL300000086955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086955 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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] 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: [56, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 99, 99, 99, 99, 99, 99, 99, 99, 99, 57, 57, 57, 11, 1, 1, 1, 99, 99, 99, 99, 99, 99, 99] 99 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086955 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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] 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: [11, 1, 11, 11, 37, 99, 99, 99, 99, 99, 99, 99, 99, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 37, 99, 99, 99, 1, 1, 1, 1, 1, 1, 1] 99 rigid atoms, others: [32, 1, 34, 35, 36, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 183 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086955 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086955 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086955/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086955 Building REAL300000086956 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086956' /scratch/stefan/7769667/working/building/REAL300000086956 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086956 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086956/0 /scratch/stefan/7769667/working/building/REAL300000086956 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/996 `/scratch/stefan/7769667/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=C(F)C=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1) `REAL300000086956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086956 none CC1=NN(C2=CC=C(F)C=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 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 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 12, 61, 138, 138, 137, 137, 138, 138, 138, 138, 2, 2, 2, 5, 5, 5, 5, 12, 61, 138, 138, 138] 178 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]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086956 none CC1=NN(C2=CC=C(F)C=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 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 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 138, 138, 178, 178, 178, 178, 178, 178, 138, 138, 64, 64, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 178, 178, 178, 178, 64, 13, 1, 1, 1] 178 rigid atoms, others: [35, 36, 37, 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]) total number of confs: 276 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086956 none CC1=NN(C2=CC=C(F)C=C2)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])N=C1 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', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 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, 4, 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 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 39, 39, 103, 178, 178, 178, 178, 178, 178, 178, 178, 5, 5, 5, 1, 1, 1, 1, 39, 103, 178, 178, 178] 178 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 389 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086956 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086956 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086956/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086956 Building REAL300000086957 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086957' /scratch/stefan/7769667/working/building/REAL300000086957 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086957 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086957/0 /scratch/stefan/7769667/working/building/REAL300000086957 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/997 `/scratch/stefan/7769667/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC=C3)N=C2C2=CC=CS2)C=N1) `REAL300000086957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086957 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC=C3)N=C2C2=CC=CS2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 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, 110, 43, 43, 12, 12, 12, 12, 12, 26, 26, 12, 26, 26, 12, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 110, 43, 12, 26, 26, 12, 26, 26, 1, 1, 1, 201] 201 rigid atoms, others: [38, 39, 40, 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, 41]) total number of confs: 492 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086957 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC=C3)N=C2C2=CC=CS2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 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] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 11, 61, 61, 133, 133, 133, 136, 136, 133, 136, 136, 133, 133, 133, 201, 201, 201, 201, 1, 1, 1, 1, 11, 61, 133, 136, 136, 134, 136, 136, 201, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086957 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC=C3)N=C2C2=CC=CS2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 136, 136, 136, 66, 18, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 26, 26, 26, 26, 136, 136, 136, 136, 66, 18, 4, 1, 1, 1, 1, 1, 26, 26, 26, 136] 201 rigid atoms, others: [33, 34, 35, 36, 37, 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, 38, 39, 40, 41]) total number of confs: 297 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086957 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC=C3)N=C2C2=CC=CS2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 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] 0 hydrogens 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, 133, 133, 133, 133, 133, 54, 13, 13, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 1, 12, 12, 12, 12, 133, 133, 133, 133, 54, 13, 1, 4, 4, 2, 4, 4, 12, 12, 12, 133] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 266 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086957 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086957 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086957/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086957 Building REAL300000086958 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086958' /scratch/stefan/7769667/working/building/REAL300000086958 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086958 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086958/0 /scratch/stefan/7769667/working/building/REAL300000086958 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/998 `/scratch/stefan/7769667/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC=C3)N=C2C2=CC=CC=C2)C=N1) `REAL300000086958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086958 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC=C3)N=C2C2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 158, 158, 158, 79, 23, 23, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 79, 23, 6, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 158] 158 rigid atoms, others: [39, 40, 41, 42, 43, 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, 44]) total number of confs: 333 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086958 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC=C3)N=C2C2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 13, 69, 69, 157, 157, 157, 158, 158, 158, 158, 158, 157, 157, 157, 158, 158, 158, 158, 158, 1, 1, 1, 1, 13, 69, 157, 158, 158, 158, 158, 158, 158, 158, 157, 158, 158, 1] 158 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086958 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC=C3)N=C2C2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 158, 158, 158, 61, 14, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 4, 9, 9, 158, 158, 158, 158, 61, 14, 4, 1, 1, 1, 1, 1, 9, 9, 4, 9, 9, 158] 158 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 307 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086958 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC=C3)N=C2C2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 157, 157, 157, 58, 11, 11, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 6, 6, 2, 6, 6, 157, 157, 157, 157, 58, 11, 1, 4, 4, 4, 4, 4, 6, 6, 1, 6, 6, 157] 158 rigid atoms, others: [33, 9, 10, 11, 12, 13, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086958 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086958 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086958/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086958 Building REAL300000086959 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086959' /scratch/stefan/7769667/working/building/REAL300000086959 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086959 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086959/0 /scratch/stefan/7769667/working/building/REAL300000086959 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/999 `/scratch/stefan/7769667/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C)C([N+](=O)[O-])=C1) `REAL300000086959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086959 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 5, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [58, 59, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 115, 115, 115, 115, 115, 115, 115, 115, 115, 59, 59, 59, 13, 1, 1, 1, 115, 115, 115, 115, 115, 115] 115 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086959 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(C)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 5, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 55, 115, 115, 115, 115, 115, 115, 115, 115, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 55, 115, 115, 115, 1, 1, 2, 2, 2, 1] 115 rigid atoms, others: [1, 35, 13, 14, 15, 16, 17, 18, 19, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 241 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086959 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086959 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086959/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086959 Building REAL300000086960 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086960' /scratch/stefan/7769667/working/building/REAL300000086960 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086960 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086960/0 /scratch/stefan/7769667/working/building/REAL300000086960 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1000 `/scratch/stefan/7769667/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(=O)C1=CC=CN=C1) `REAL300000086960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086960 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(=O)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 7, 5, 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: [3, 1, 1, 1, 1, 1, 6, 6, 12, 29, 29, 28, 29, 29, 29, 29, 29, 1, 1, 1, 1, 7, 15, 15, 45, 45, 45, 45, 45, 4, 4, 4, 1, 6, 12, 29, 29, 29, 1, 1, 45, 45, 45, 45] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 38, 39, 17, 18, 19, 20] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086960 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(=O)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 7, 5, 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: [82, 45, 45, 45, 35, 45, 88, 88, 117, 201, 201, 201, 201, 201, 201, 201, 201, 45, 45, 25, 6, 1, 6, 1, 1, 1, 1, 1, 1, 82, 82, 82, 45, 88, 117, 201, 201, 201, 45, 45, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 21, 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, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 605 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086960 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(=O)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 7, 5, 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: [53, 29, 29, 29, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 86, 116, 116, 201, 201, 201, 201, 201, 53, 53, 53, 29, 13, 7, 1, 1, 1, 29, 29, 201, 201, 201, 201] 201 rigid atoms, others: [35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 434 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086960 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086960 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086960/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086960 Building REAL300000086961 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086961' /scratch/stefan/7769667/working/building/REAL300000086961 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086961 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086961/0 /scratch/stefan/7769667/working/building/REAL300000086961 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1001 `/scratch/stefan/7769667/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C2C(=C1)CC1=CC=CC=C12) `REAL300000086961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086961 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [52, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 83, 83, 70, 83, 83, 83, 83, 83, 83, 83, 83, 83, 53, 53, 53, 11, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83, 83, 83] 83 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 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]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086961 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 37, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 37, 83, 83, 83, 1, 1, 1, 1, 1, 1, 1, 1, 1] 83 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29, 30, 31]) total number of confs: 175 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086961 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086961 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086961/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086961 Building REAL300000086962 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086962' /scratch/stefan/7769667/working/building/REAL300000086962 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086962 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086962/0 /scratch/stefan/7769667/working/building/REAL300000086962 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1002 `/scratch/stefan/7769667/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OC)C(OC)=C1) `REAL300000086962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086962 none CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OC)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 7, 7, 7] 0 hydrogens 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, 28, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 134, 134, 134, 134, 168, 134, 134, 171, 134, 49, 49, 49, 49, 49, 7, 1, 1, 1, 134, 134, 168, 168, 168, 171, 171, 171, 134] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 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]) total number of confs: 440 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086962 none CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OC)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 7, 7, 7] 0 hydrogens 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, 13, 1, 13, 13, 60, 134, 134, 134, 134, 134, 134, 134, 134, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 27, 27, 27, 27, 27, 60, 134, 134, 134, 1, 1, 3, 3, 3, 4, 4, 4, 1] 201 rigid atoms, others: [33, 2, 41, 34, 14, 15, 16, 17, 18, 20, 21, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 365 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086962 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086962 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086962/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086962 Building REAL300000086963 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086963' /scratch/stefan/7769667/working/building/REAL300000086963 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086963 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086963/0 /scratch/stefan/7769667/working/building/REAL300000086963 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1003 `/scratch/stefan/7769667/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21) `REAL300000086963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086963 none CC(C)N1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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: [5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 21, 21, 20, 20, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 3, 3, 3, 2, 2, 2, 2, 7, 21, 21, 21, 1, 1, 1, 1] 21 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 36, 38, 37, 35] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086963 none CC(C)N1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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: [5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 20, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 20, 21, 21, 21, 9, 1, 1, 1, 21, 21, 21, 21] 21 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086963 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086963 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086963/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086963 Building REAL300000086964 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086964' /scratch/stefan/7769667/working/building/REAL300000086964 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086964 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086964/0 /scratch/stefan/7769667/working/building/REAL300000086964 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1004 `/scratch/stefan/7769667/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCN1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21) `REAL300000086964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086964 none CC(C)CCN1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [13, 11, 15, 8, 1, 1, 1, 1, 1, 1, 1, 7, 37, 37, 36, 36, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 15, 15, 13, 15, 15, 15, 15, 11, 11, 8, 8, 7, 37, 37, 37, 1, 1, 1, 1] 85 rigid atoms, others: [43, 4, 5, 6, 7, 8, 9, 10, 23, 44, 20, 21, 22, 41, 24, 25, 42] set([0, 1, 2, 3, 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086964 none CC(C)CCN1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [84, 85, 85, 81, 37, 37, 36, 37, 37, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 85, 85, 84, 85, 85, 85, 85, 85, 85, 81, 81, 12, 1, 1, 1, 37, 37, 37, 37] 85 rigid atoms, others: [38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44]) total number of confs: 296 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086964 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086964 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086964/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086964 Building REAL300000086965 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086965' /scratch/stefan/7769667/working/building/REAL300000086965 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086965 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086965/0 /scratch/stefan/7769667/working/building/REAL300000086965 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1005 `/scratch/stefan/7769667/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OC(F)F)C=C1) `REAL300000086965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086965 none CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens 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, 22, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 64, 64, 28, 64, 148, 171, 171, 64, 64, 33, 33, 33, 33, 33, 7, 1, 1, 1, 64, 64, 171, 64, 64] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 520 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086965 none CCC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens 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, 7, 1, 7, 7, 30, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 10, 21, 21, 1, 1, 11, 11, 11, 11, 11, 30, 64, 64, 64, 1, 1, 20, 1, 1] 201 rigid atoms, others: [33, 2, 36, 37, 34, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 215 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086965 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086965 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086965/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086965 Building REAL300000086966 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086966' /scratch/stefan/7769667/working/building/REAL300000086966 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086966 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086966/0 /scratch/stefan/7769667/working/building/REAL300000086966 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1006 `/scratch/stefan/7769667/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(N3CCC(C4=CC=CC=C4)=N3)C=C2)C=N1) `REAL300000086966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086966 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3CCC(C4=CC=CC=C4)=N3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 156, 156, 156, 94, 54, 54, 33, 10, 33, 33, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 33, 33, 156, 156, 156, 156, 94, 54, 33, 33, 7, 7, 7, 7, 1, 1, 1, 1, 1, 33, 33, 156] 156 rigid atoms, others: [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, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 415 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086966 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3CCC(C4=CC=CC=C4)=N3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 50, 50, 95, 95, 95, 95, 145, 145, 145, 145, 156, 156, 156, 156, 156, 145, 95, 95, 1, 1, 1, 1, 12, 50, 95, 95, 145, 145, 145, 145, 156, 156, 156, 156, 156, 95, 95, 1] 156 rigid atoms, others: [1, 3, 4, 5, 6, 7, 46, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086966 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3CCC(C4=CC=CC=C4)=N3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 145, 145, 145, 69, 18, 18, 8, 1, 9, 9, 1, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 1, 9, 9, 145, 145, 145, 145, 69, 18, 9, 9, 1, 1, 1, 1, 7, 7, 3, 7, 7, 9, 9, 145] 156 rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 336 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086966 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3CCC(C4=CC=CC=C4)=N3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 95, 95, 30, 4, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 33, 33, 9, 33, 33, 9, 1, 1, 95, 95, 95, 95, 30, 4, 1, 1, 9, 9, 9, 9, 33, 33, 12, 33, 33, 1, 1, 95] 156 rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 14, 44, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086966 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086966 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086966/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086966 Building REAL300000086967 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086967' /scratch/stefan/7769667/working/building/REAL300000086967 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086967 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086967/0 /scratch/stefan/7769667/working/building/REAL300000086967 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1007 `/scratch/stefan/7769667/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C2=CC=CC=C2C(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1C1=CC=CC=C1) `REAL300000086967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086967 none CN1C2=CC=CC=C2C(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 59, 146, 146, 146, 146, 146, 146, 146, 146, 1, 1, 4, 4, 1, 4, 4, 2, 2, 2, 1, 1, 1, 1, 13, 59, 146, 146, 146, 4, 4, 1, 4, 4] 146 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 34, 21, 22, 33, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086967 none CN1C2=CC=CC=C2C(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 79, 146, 146, 146, 146, 146, 146, 146, 146, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 29, 79, 146, 146, 146, 1, 1, 1, 1, 1] 146 rigid atoms, others: [40, 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]) total number of confs: 321 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086967 none CN1C2=CC=CC=C2C(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 146, 146, 146, 146, 67, 67, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 67, 13, 1, 1, 1, 146, 146, 146, 146, 146] 146 rigid atoms, others: [37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086967 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086967 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086967/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086967 Building REAL300000086968 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086968' /scratch/stefan/7769667/working/building/REAL300000086968 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086968 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086968/0 /scratch/stefan/7769667/working/building/REAL300000086968 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1008 `/scratch/stefan/7769667/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(S(N)(=O)=O)C=C1) `REAL300000086968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086968 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(S(N)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [52, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 79, 79, 54, 54, 177, 177, 177, 79, 79, 53, 53, 53, 11, 1, 1, 1, 79, 79, 177, 177, 79, 79] 181 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 668 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086968 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(S(N)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 25, 79, 79, 79, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 6, 6, 6, 25, 79, 79, 79, 1, 1, 5, 5, 1, 1] 181 rigid atoms, others: [1, 34, 35, 13, 14, 15, 16, 17, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 155 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086968 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086968 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086968/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086968 Building REAL300000086969 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086969' /scratch/stefan/7769667/working/building/REAL300000086969 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086969 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086969/0 /scratch/stefan/7769667/working/building/REAL300000086969 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1009 `/scratch/stefan/7769667/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C([N+](=O)[O-])=C2)C=N1) `REAL300000086969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086969 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C([N+](=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 8, 11, 11, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 11, 43, 43, 73, 73, 43, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1, 11, 43, 73, 73, 73, 1] 73 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086969 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C([N+](=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 8, 11, 11, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 73, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 73, 73, 73, 73, 31, 9, 1, 1, 1, 73] 73 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086969 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086969 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086969/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086969 Building REAL300000086970 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086970' /scratch/stefan/7769667/working/building/REAL300000086970 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086970 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086970/0 /scratch/stefan/7769667/working/building/REAL300000086970 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1010 `/scratch/stefan/7769667/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1Br) `REAL300000086970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086970 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1Br 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 11, 11, 8, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [3, 1, 1, 1, 1, 1, 1, 10, 10, 51, 132, 132, 131, 132, 132, 132, 132, 132, 1, 1, 1, 3, 3, 3, 1, 1, 10, 51, 132, 132, 132, 1] 151 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086970 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1Br 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 11, 11, 8, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 132, 115, 132, 132, 72, 72, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 151, 151, 151, 132, 132, 72, 13, 1, 1, 1, 132] 151 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 319 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086970 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086970 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086970/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086970 Building REAL300000086971 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086971' /scratch/stefan/7769667/working/building/REAL300000086971 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086971 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086971/0 /scratch/stefan/7769667/working/building/REAL300000086971 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1011 `/scratch/stefan/7769667/working/3D/1011' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=CC(C=NNC3=CC=C(C(=O)[O-])N=C3)=C(Cl)N=C2C=C1) `REAL300000086971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086971 none COC1=CC2=CC(C=NNC3=CC=C(C(=O)[O-])N=C3)=C(Cl)N=C2C=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 11, 11, 8, 1, 1, 16, 8, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 10, 30, 83, 83, 83, 1, 1] 83 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 36, 28, 29, 35] set([0, 32, 34, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 30, 31]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086971 none COC1=CC2=CC(C=NNC3=CC=C(C(=O)[O-])N=C3)=C(Cl)N=C2C=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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, 11, 11, 8, 1, 1, 16, 8, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 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: [83, 83, 83, 83, 83, 83, 53, 53, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 53, 13, 1, 1, 1, 83, 83] 83 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086971 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086971 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086971/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086971 Building REAL300000086972 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086972' /scratch/stefan/7769667/working/building/REAL300000086972 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086972 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086972/0 /scratch/stefan/7769667/working/building/REAL300000086972 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1012 `/scratch/stefan/7769667/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1C[NH+]1CCCCC1) `REAL300000086972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086972 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1C[NH+]1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 9, 6, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 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: [3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 38, 61, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 3, 3, 3, 1, 1, 12, 12, 12, 38, 61, 61, 61, 1, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 147 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 41, 19, 20, 21] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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, 50, 51, 52, 53]) total number of confs: 180 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: REAL300000086972 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1C[NH+]1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 9, 6, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 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: [19, 9, 9, 9, 9, 9, 9, 48, 48, 48, 108, 147, 147, 147, 147, 147, 147, 147, 147, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 9, 9, 48, 48, 48, 108, 147, 147, 147, 9, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 147 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 378 number of broken/clashed sets: 52 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086972 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1C[NH+]1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 9, 6, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 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: [73, 27, 25, 61, 61, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 118, 147, 147, 147, 147, 147, 147, 73, 73, 73, 61, 61, 19, 19, 19, 7, 1, 1, 1, 61, 118, 118, 147, 147, 147, 147, 147, 147, 147, 147, 147, 147] 147 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 604 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086972 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086972 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086972/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086972 Building REAL300000086973 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086973' /scratch/stefan/7769667/working/building/REAL300000086973 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086973 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086973/0 /scratch/stefan/7769667/working/building/REAL300000086973 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1013 `/scratch/stefan/7769667/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1C[NH+]1CCCC1) `REAL300000086973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086973 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1C[NH+]1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 9, 6, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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] 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, 1, 12, 12, 12, 33, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 5, 10, 10, 10, 10, 10, 4, 4, 4, 1, 1, 13, 13, 13, 33, 62, 62, 62, 1, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10] 139 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 40, 19, 20, 21, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 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: REAL300000086973 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1C[NH+]1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 9, 6, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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] 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: [20, 10, 10, 10, 10, 10, 10, 47, 47, 47, 97, 139, 139, 139, 139, 139, 139, 139, 139, 10, 5, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 10, 10, 47, 47, 47, 97, 139, 139, 139, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 139 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 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, 42]) total number of confs: 355 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086973 none COC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)C=C1C[NH+]1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 9, 6, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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] 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: [75, 62, 35, 62, 62, 25, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 104, 139, 139, 139, 139, 139, 75, 75, 75, 62, 62, 25, 25, 25, 7, 1, 1, 1, 62, 104, 104, 139, 139, 139, 139, 139, 139, 139, 139] 139 rigid atoms, others: [37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 568 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086973 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086973 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086973/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086973 Building REAL300000086974 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086974' /scratch/stefan/7769667/working/building/REAL300000086974 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086974 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086974/0 /scratch/stefan/7769667/working/building/REAL300000086974 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1014 `/scratch/stefan/7769667/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C1=NC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CS1)C1=CC=CC=C1) `REAL300000086974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086974 none CC(=O)N(C1=NC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CS1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [21, 7, 21, 1, 1, 1, 1, 1, 6, 6, 27, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 7, 18, 18, 11, 18, 18, 21, 21, 21, 6, 26, 64, 64, 64, 1, 18, 18, 11, 18, 18] 201 rigid atoms, others: [35, 3, 4, 5, 6, 7, 19, 20] set([0, 1, 2, 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, 36, 37, 38, 39, 40]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086974 none CC(=O)N(C1=NC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CS1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [17, 6, 17, 1, 6, 18, 18, 18, 39, 39, 110, 199, 199, 199, 199, 199, 199, 199, 199, 18, 18, 1, 1, 1, 1, 1, 1, 17, 17, 17, 39, 110, 199, 199, 199, 18, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 36, 37, 38, 39, 40, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 469 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086974 none CC(=O)N(C1=NC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CS1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 145, 201, 64, 64, 60, 37, 37, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 64, 64, 145, 199, 199, 173, 199, 199, 201, 201, 201, 37, 11, 1, 1, 1, 64, 199, 199, 180, 199, 199] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 741 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086974 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086974 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086974/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086974 Building REAL300000086975 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086975' /scratch/stefan/7769667/working/building/REAL300000086975 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086975 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086975/0 /scratch/stefan/7769667/working/building/REAL300000086975 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1015 `/scratch/stefan/7769667/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CSC(C3=CC=C(Cl)C=C3)=N2)C=N1) `REAL300000086975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086975 none O=C([O-])C1=CC=C(NN=CC2=CSC(C3=CC=C(Cl)C=C3)=N2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 52, 52, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1, 12, 52, 73, 73, 73, 73, 73, 1] 73 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086975 none O=C([O-])C1=CC=C(NN=CC2=CSC(C3=CC=C(Cl)C=C3)=N2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 73, 36, 15, 15, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 73, 73, 73, 73, 36, 15, 4, 1, 1, 1, 1, 73] 73 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 33]) total number of confs: 147 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086975 none O=C([O-])C1=CC=C(NN=CC2=CSC(C3=CC=C(Cl)C=C3)=N2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 73, 31, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 73, 73, 73, 73, 31, 7, 1, 4, 4, 4, 4, 73] 73 rigid atoms, others: [9, 10, 11, 12, 13, 14, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086975 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086975 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086975/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086975 Building REAL300000086976 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086976' /scratch/stefan/7769667/working/building/REAL300000086976 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086976 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086976/0 /scratch/stefan/7769667/working/building/REAL300000086976 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1016 `/scratch/stefan/7769667/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(N3CCCCC3)N=C3C=CC=CN3C2=O)C=N1) `REAL300000086976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086976 none O=C([O-])C1=CC=C(NN=CC2=C(N3CCCCC3)N=C3C=CC=CN3C2=O)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', '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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 33, 33, 63, 63, 87, 87, 87, 87, 87, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 11, 33, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 63, 63, 63, 63, 1] 87 rigid atoms, others: [1, 3, 4, 5, 6, 7, 47, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086976 none O=C([O-])C1=CC=C(NN=CC2=C(N3CCCCC3)N=C3C=CC=CN3C2=O)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', '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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 87, 87, 56, 30, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 87, 87, 87, 87, 56, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 87] 87 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086976 none O=C([O-])C1=CC=C(NN=CC2=C(N3CCCCC3)N=C3C=CC=CN3C2=O)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', '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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 32, 8, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 32, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 63] 87 rigid atoms, others: [43, 9, 10, 11, 12, 45, 46, 44, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47]) total number of confs: 134 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086976 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086976 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086976/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086976 Building REAL300000086977 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086977' /scratch/stefan/7769667/working/building/REAL300000086977 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086977 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086977/0 /scratch/stefan/7769667/working/building/REAL300000086977 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1017 `/scratch/stefan/7769667/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C2=NC(C=NNC3=CC=C(C(=O)[O-])N=C3)=CS2)=C1) `REAL300000086977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086977 none COC1=CC=CC(C2=NC(C=NNC3=CC=C(C(=O)[O-])N=C3)=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 14, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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, 1, 5, 5, 5, 23, 23, 75, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 1, 3, 3, 3, 1, 1, 1, 23, 75, 201, 201, 201, 5, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 24, 28, 29, 30, 37] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086977 none COC1=CC=CC(C2=NC(C=NNC3=CC=C(C(=O)[O-])N=C3)=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 14, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 110, 110, 110, 66, 66, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 110, 110, 201, 201, 201, 201, 201, 201, 201, 66, 11, 1, 1, 1, 110, 201] 201 rigid atoms, others: [33, 34, 35, 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, 36, 37]) total number of confs: 292 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086977 none COC1=CC=CC(C2=NC(C=NNC3=CC=C(C(=O)[O-])N=C3)=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 14, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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, 5, 5, 4, 5, 5, 1, 1, 1, 1, 1, 6, 6, 33, 110, 110, 110, 110, 110, 110, 110, 110, 1, 1, 5, 9, 9, 9, 4, 5, 5, 6, 33, 110, 110, 110, 1, 5] 201 rigid atoms, others: [36, 6, 7, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086977 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086977 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086977/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086977 Building REAL300000086978 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086978' /scratch/stefan/7769667/working/building/REAL300000086978 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086978 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086978/0 /scratch/stefan/7769667/working/building/REAL300000086978 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1018 `/scratch/stefan/7769667/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(C)=NNC3=CC=C(C(=O)[O-])N=C3)=CC2=CC=C1) `REAL300000086978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086978 none COC1=C2OC(C(C)=NNC3=CC=C(C(=O)[O-])N=C3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', '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, 12, 1, 1, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 44, 131, 131, 131, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 43, 131, 131, 131, 1, 1, 1, 1] 131 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 19, 20, 21, 22, 23, 36, 37, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 245 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086978 none COC1=C2OC(C(C)=NNC3=CC=C(C(=O)[O-])N=C3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', '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, 12, 1, 1, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 131, 131, 65, 65, 64, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 131, 131, 131, 65, 65, 65, 13, 1, 1, 1, 131, 131, 131, 131] 131 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 198 number of broken/clashed sets: 53 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086978 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086978 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086978/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086978 Building REAL300000086979 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086979' /scratch/stefan/7769667/working/building/REAL300000086979 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086979 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086979/0 /scratch/stefan/7769667/working/building/REAL300000086979 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1019 `/scratch/stefan/7769667/working/3D/1019' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=C2OC(C(C)=NNC3=CC=C(C(=O)[O-])N=C3)=CC2=CC=C1) `REAL300000086979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086979 none CCOC1=C2OC(C(C)=NNC3=CC=C(C(=O)[O-])N=C3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [41, 12, 1, 1, 1, 1, 1, 1, 8, 8, 8, 36, 122, 122, 122, 122, 122, 122, 122, 122, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 9, 9, 9, 35, 122, 122, 122, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 39, 20, 21, 22, 23, 24, 38, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 336 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086979 none CCOC1=C2OC(C(C)=NNC3=CC=C(C(=O)[O-])N=C3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 184, 122, 122, 122, 122, 55, 55, 54, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 122, 201, 201, 201, 201, 201, 55, 55, 55, 11, 1, 1, 1, 122, 122, 122, 122] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 400 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086979 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086979 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086979/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086979 Building REAL300000086980 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086980' /scratch/stefan/7769667/working/building/REAL300000086980 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086980 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086980/0 /scratch/stefan/7769667/working/building/REAL300000086980 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1020 `/scratch/stefan/7769667/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(F)F) `REAL300000086980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086980 none CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [28, 10, 1, 1, 1, 1, 1, 6, 6, 15, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 9, 36, 36, 28, 28, 28, 28, 28, 1, 6, 14, 27, 27, 27, 1, 1, 36] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 19, 20, 21, 36, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 38]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086980 none CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [124, 89, 27, 27, 27, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 95, 172, 172, 124, 124, 124, 124, 124, 27, 11, 7, 1, 1, 1, 27, 27, 172] 201 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 771 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086980 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086980 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086980/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086980 Building REAL300000086981 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086981' /scratch/stefan/7769667/working/building/REAL300000086981 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086981 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086981/0 /scratch/stefan/7769667/working/building/REAL300000086981 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1021 `/scratch/stefan/7769667/working/3D/1021' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1) `REAL300000086981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086981 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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', '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, 11, 11, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 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: [29, 30, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 72, 72, 30, 50, 103, 103, 103, 142, 152, 152, 152, 72, 72, 30, 30, 30, 7, 1, 1, 1, 72, 72, 142, 152, 152, 72, 72] 152 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 696 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086981 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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', '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, 11, 11, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 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: [6, 1, 6, 6, 26, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 19, 19, 1, 1, 6, 6, 6, 26, 72, 72, 72, 1, 1, 9, 17, 17, 1, 1] 152 rigid atoms, others: [1, 34, 35, 39, 40, 13, 14, 15, 16, 17, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 209 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086981 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086981 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086981/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086981 Building REAL300000086982 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086982' /scratch/stefan/7769667/working/building/REAL300000086982 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086982 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086982/0 /scratch/stefan/7769667/working/building/REAL300000086982 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1022 `/scratch/stefan/7769667/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(O)C(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1) `REAL300000086982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086982 none CCOC1=CC=C(O)C(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 252 conformations in input total number of sets (complete confs): 252 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 31, 91, 91, 91, 91, 91, 91, 91, 91, 1, 15, 15, 15, 15, 15, 1, 1, 2, 6, 31, 91, 91, 91, 1] 252 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 35, 21, 27, 28] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 201 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086982 none CCOC1=CC=C(O)C(C=NNC2=CC=C(C(=O)[O-])N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 252 conformations in input total number of sets (complete confs): 252 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 91, 91, 91, 91, 91, 91, 54, 54, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 91, 126, 126, 126, 126, 126, 91, 91, 182, 54, 12, 1, 1, 1, 91] 252 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 386 number of broken/clashed sets: 75 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086982 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086982 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086982/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086982 Building REAL300000086983 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086983' /scratch/stefan/7769667/working/building/REAL300000086983 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086983 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086983/0 /scratch/stefan/7769667/working/building/REAL300000086983 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1023 `/scratch/stefan/7769667/working/3D/1023' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(C)=C1OC(F)F) `REAL300000086983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086983 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(C)=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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, 1, 12, 12, 59, 152, 152, 152, 152, 152, 152, 152, 152, 1, 1, 1, 1, 1, 4, 14, 14, 2, 2, 2, 1, 12, 59, 152, 152, 152, 1, 2, 2, 2, 14] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 16, 17, 18, 19, 20, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086983 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(C)=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [152, 152, 152, 67, 67, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 152, 152, 152, 113, 113, 183, 201, 201, 152, 152, 152, 152, 67, 12, 1, 1, 1, 152, 152, 152, 152, 201] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 566 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086983 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086983 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086983/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086983 Building REAL300000086984 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086984' /scratch/stefan/7769667/working/building/REAL300000086984 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086984 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086984/0 /scratch/stefan/7769667/working/building/REAL300000086984 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1024 `/scratch/stefan/7769667/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOC1=CC=C(Br)C=C1C=NNC1=CC=C(C(=O)[O-])N=C1) `REAL300000086984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086984 none C#CCOC1=CC=C(Br)C=C1C=NNC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 34, 86, 86, 86, 86, 86, 86, 86, 86, 39, 39, 39, 1, 1, 1, 8, 34, 86, 86, 86] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086984 none C#CCOC1=CC=C(Br)C=C1C=NNC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 141, 86, 86, 86, 47, 86, 86, 86, 43, 43, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 86, 86, 86, 43, 11, 1, 1, 1] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 717 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086984 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086984 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086984/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086984 Building REAL300000086985 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086985' /scratch/stefan/7769667/working/building/REAL300000086985 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086985 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086985/0 /scratch/stefan/7769667/working/building/REAL300000086985 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1025 `/scratch/stefan/7769667/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(F)F) `REAL300000086985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086985 none COC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [3, 1, 1, 1, 1, 1, 11, 11, 11, 42, 89, 89, 89, 89, 89, 89, 89, 89, 1, 1, 1, 1, 9, 28, 28, 3, 3, 3, 1, 11, 11, 11, 42, 89, 89, 89, 1, 1, 28] 201 rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 20, 21, 36, 28, 37] set([0, 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, 38]) total number of confs: 263 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086985 none COC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 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: [139, 89, 89, 89, 32, 32, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 161, 201, 201, 139, 139, 139, 89, 32, 32, 32, 7, 1, 1, 1, 89, 89, 201] 201 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 547 number of broken/clashed sets: 82 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086985 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086985 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086985/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086985 Building REAL300000086986 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086986' /scratch/stefan/7769667/working/building/REAL300000086986 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086986 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086986/0 /scratch/stefan/7769667/working/building/REAL300000086986 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1026 `/scratch/stefan/7769667/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC3=CC=CC=C3N=C2N2CCOCC2)C=N1) `REAL300000086986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086986 none O=C([O-])C1=CC=C(NN=CC2=CC3=CC=CC=C3N=C2N2CCOCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 12, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1] 30 rigid atoms, others: [1, 3, 4, 5, 6, 7, 45, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 60 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086986 none O=C([O-])C1=CC=C(NN=CC2=CC3=CC=CC=C3N=C2N2CCOCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 16, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 16, 6, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 30] 30 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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, 45]) total number of confs: 66 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086986 none O=C([O-])C1=CC=C(NN=CC2=CC3=CC=CC=C3N=C2N2CCOCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 30, 30, 30, 30, 13, 4, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 30] 30 rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 61 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086986 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086986 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086986/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086986 Building REAL300000086987 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086987' /scratch/stefan/7769667/working/building/REAL300000086987 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000086987 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086987/0 /scratch/stefan/7769667/working/building/REAL300000086987 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1027 `/scratch/stefan/7769667/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC(C)C) `REAL300000086987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086987 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', '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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 5, 5, 5, 5, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 34, 84, 84, 84, 84, 84, 84, 84, 84, 1, 1, 1, 1, 3, 3, 3, 2, 2, 2, 1, 9, 34, 84, 84, 84, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 104 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086987 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', '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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 5, 5, 5, 5, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 49, 49, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 104, 104, 104, 84, 84, 84, 84, 49, 13, 1, 1, 1, 84, 84, 84, 104, 104, 104, 104, 104, 104, 104, 104, 104] 104 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 259 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086987 /scratch/stefan/7769667/working /scratch/stefan/7769667 mkdir: created directory `1' /scratch/stefan/7769667/working/building/REAL300000086987/1 /scratch/stefan/7769667/working/building/REAL300000086987 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 1 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1028 `/scratch/stefan/7769667/working/3D/1028' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC(C)C) `REAL300000086987.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000086987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086987 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', '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, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 47, 48, 94, 94, 94, 94, 94, 94, 94, 94, 1, 1, 1, 1, 2, 5, 5, 2, 2, 2, 1, 9, 9, 94, 94, 94, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5] 162 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086987 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])N=C2)=C(C)N1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', '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, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 39, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 159, 162, 162, 94, 94, 94, 94, 38, 39, 1, 1, 1, 94, 94, 94, 159, 159, 162, 162, 162, 162, 162, 162, 162] 162 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 605 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086987 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086987 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086987/0.* 1: /scratch/stefan/7769667/working/building/REAL300000086987/1.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086987 Building REAL300000086988 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086988' /scratch/stefan/7769667/working/building/REAL300000086988 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086988 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086988/0 /scratch/stefan/7769667/working/building/REAL300000086988 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1029 `/scratch/stefan/7769667/working/3D/1029' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)SC(N2CCCCC2)=N1) `REAL300000086988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086988 none CC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)SC(N2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'S.3', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 14, 1, 8, 5, 5, 5, 5, 5, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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, 11, 11, 61, 140, 140, 140, 140, 140, 140, 140, 139, 1, 1, 1, 12, 12, 12, 12, 12, 1, 2, 2, 2, 11, 61, 140, 140, 140, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 201 rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 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: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086988 none CC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)SC(N2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'S.3', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 14, 1, 8, 5, 5, 5, 5, 5, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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: [12, 12, 12, 12, 61, 61, 117, 201, 201, 201, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 61, 117, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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]) total number of confs: 468 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086988 none CC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)SC(N2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'S.3', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 14, 1, 8, 5, 5, 5, 5, 5, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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: [140, 140, 60, 60, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 201, 201, 201, 201, 201, 131, 140, 140, 140, 60, 11, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086988 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086988 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086988/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086988 Building REAL300000086989 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086989' /scratch/stefan/7769667/working/building/REAL300000086989 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086989 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086989/0 /scratch/stefan/7769667/working/building/REAL300000086989 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1030) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1030 `/scratch/stefan/7769667/working/3D/1030' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OCC(=O)N2CCCCC2)C=C1) `REAL300000086989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086989 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OCC(=O)N2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 30, 30, 17, 20, 77, 132, 201, 201, 201, 201, 201, 201, 201, 30, 30, 12, 12, 12, 5, 1, 1, 1, 30, 30, 130, 130, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 30, 30] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 35] set([0, 1, 2, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 651 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: REAL300000086989 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OCC(=O)N2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 46, 104, 106, 116, 201, 201, 201, 201, 201, 201, 201, 201, 31, 57, 57, 31, 11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 57, 57, 106, 106, 106, 116, 201, 201, 201, 57, 57, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57] 201 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 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, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 50, 51]) total number of confs: 579 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086989 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=C(OCC(=O)N2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 15, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 6, 16, 51, 51, 57, 57, 57, 57, 57, 1, 1, 5, 5, 5, 15, 30, 30, 30, 1, 1, 16, 16, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1] 201 rigid atoms, others: [1, 36, 37, 13, 14, 15, 16, 17, 50, 51, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086989 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086989 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086989/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086989 Building REAL300000086990 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086990' /scratch/stefan/7769667/working/building/REAL300000086990 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086990 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086990/0 /scratch/stefan/7769667/working/building/REAL300000086990 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1031) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1031 `/scratch/stefan/7769667/working/3D/1031' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(N2C=NN=N2)=C1) `REAL300000086990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086990 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(N2C=NN=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [41, 42, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 102, 102, 102, 102, 102, 141, 141, 141, 141, 102, 42, 42, 42, 11, 1, 1, 1, 102, 102, 102, 141, 102] 141 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 236 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: REAL300000086990 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(N2C=NN=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 23, 23, 78, 141, 141, 141, 141, 141, 141, 141, 141, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 23, 23, 23, 78, 141, 141, 141, 5, 5, 5, 1, 5] 141 rigid atoms, others: [34, 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, 35]) total number of confs: 310 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086990 none CC(=NNC1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(N2C=NN=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', '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, 11, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 49, 102, 102, 102, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 11, 49, 102, 102, 102, 1, 1, 1, 5, 1] 141 rigid atoms, others: [32, 1, 35, 33, 13, 14, 15, 16, 17, 18, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 215 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086990 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086990 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086990/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086990 Building REAL300000086991 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086991' /scratch/stefan/7769667/working/building/REAL300000086991 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086991 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086991/0 /scratch/stefan/7769667/working/building/REAL300000086991 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1032) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1032 `/scratch/stefan/7769667/working/3D/1032' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)SC(N2CCOCC2)=N1) `REAL300000086991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086991 none CC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)SC(N2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'S.3', 'C.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 14, 1, 8, 5, 5, 12, 5, 5, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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, 11, 11, 53, 137, 137, 136, 136, 137, 137, 137, 137, 1, 1, 1, 13, 13, 13, 13, 13, 1, 2, 2, 2, 11, 53, 137, 137, 137, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 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: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086991 none CC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)SC(N2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'S.3', 'C.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 14, 1, 8, 5, 5, 12, 5, 5, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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: [13, 13, 13, 13, 65, 65, 117, 201, 201, 201, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 65, 117, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 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]) total number of confs: 465 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086991 none CC1=C(C=NNC2=CC=C(C(=O)[O-])N=C2)SC(N2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'S.3', 'C.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 14, 1, 8, 5, 5, 12, 5, 5, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 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: [137, 137, 58, 58, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 201, 201, 201, 201, 201, 127, 137, 137, 137, 58, 11, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 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: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086991 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086991 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086991/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086991 Building REAL300000086992 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086992' /scratch/stefan/7769667/working/building/REAL300000086992 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086992 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086992/0 /scratch/stefan/7769667/working/building/REAL300000086992 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1033) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1033 `/scratch/stefan/7769667/working/3D/1033' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(O)C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=C1) `REAL300000086992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086992 none COC1=CC=C(O)C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 374 conformations in input total number of sets (complete confs): 374 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 69, 176, 176, 176, 176, 176, 176, 176, 176, 1, 3, 3, 3, 1, 1, 2, 13, 13, 13, 69, 176, 176, 176, 1] 374 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 35, 21, 25, 26] set([0, 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: 333 number of broken/clashed sets: 219 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086992 none COC1=CC=C(O)C(C(C)=NNC2=CC=C(C(=O)[O-])N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 374 conformations in input total number of sets (complete confs): 374 using faster count positions algorithm for large data unique positions, atoms: [187, 176, 176, 176, 176, 176, 176, 63, 63, 63, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 176, 187, 187, 187, 176, 176, 352, 63, 63, 63, 13, 1, 1, 1, 176] 374 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 623 number of broken/clashed sets: 219 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086992 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086992 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086992/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086992 Building REAL300000086993 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086993' /scratch/stefan/7769667/working/building/REAL300000086993 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086993 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086993/0 /scratch/stefan/7769667/working/building/REAL300000086993 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1034) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1034 `/scratch/stefan/7769667/working/3D/1034' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCO)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1) `REAL300000086993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086993 none CN(CCO)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 11, 18, 1, 1, 1, 1, 1, 6, 6, 36, 108, 108, 107, 107, 108, 108, 108, 108, 1, 1, 3, 3, 3, 11, 11, 18, 18, 54, 1, 1, 6, 36, 108, 108, 108, 1, 1] 603 rigid atoms, others: [32, 1, 5, 6, 7, 8, 9, 39, 21, 22, 38, 31] set([0, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 324 number of broken/clashed sets: 603 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086993 none CN(CCO)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.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, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [146, 70, 146, 201, 201, 70, 108, 108, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 108, 146, 146, 146, 201, 201, 201, 201, 603, 108, 108, 40, 10, 1, 1, 1, 108, 108] 603 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 1420 number of broken/clashed sets: 603 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086993 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086993 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086993/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086993 Building REAL300000086994 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086994' /scratch/stefan/7769667/working/building/REAL300000086994 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086994 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086994/0 /scratch/stefan/7769667/working/building/REAL300000086994 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1035) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1035 `/scratch/stefan/7769667/working/3D/1035' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1O) `REAL300000086994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086994 none COC1=CC(Br)=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 41, 85, 85, 85, 85, 85, 85, 85, 85, 1, 1, 1, 3, 3, 3, 1, 10, 41, 85, 85, 85, 1, 2] 170 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 25, 31] set([0, 32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086994 none COC1=CC(Br)=C(C=NNC2=CC=C(C(=O)[O-])N=C2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 85, 85, 85, 46, 46, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 84, 85, 85, 85, 46, 12, 1, 1, 1, 85, 170] 170 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086994 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086994 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086994/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086994 Building REAL300000086995 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086995' /scratch/stefan/7769667/working/building/REAL300000086995 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086995 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086995/0 /scratch/stefan/7769667/working/building/REAL300000086995 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1036) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1036 `/scratch/stefan/7769667/working/3D/1036' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(C)N=NC2=CC=C(C(=O)[O-])N=C2)C=C1OC) `REAL300000086995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086995 none COC1=CC=C(CC(C)N=NC2=CC=C(C(=O)[O-])N=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 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, 2, 11, 11, 63, 63, 140, 140, 140, 140, 140, 140, 140, 140, 1, 1, 1, 3, 3, 3, 3, 1, 1, 2, 2, 11, 11, 11, 11, 140, 140, 140, 1, 4, 4, 4] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 38, 20, 21, 22, 27, 28] 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, 37, 39, 40, 41]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086995 none COC1=CC=C(CC(C)N=NC2=CC=C(C(=O)[O-])N=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 140, 140, 140, 140, 89, 42, 9, 42, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 201, 201, 201, 201, 140, 140, 89, 89, 42, 42, 42, 42, 1, 1, 1, 140, 201, 201, 201] 201 rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 678 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086995 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086995 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086995/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086995 Building REAL300000086996 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086996' /scratch/stefan/7769667/working/building/REAL300000086996 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086996 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086996/0 /scratch/stefan/7769667/working/building/REAL300000086996 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1037) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1037 `/scratch/stefan/7769667/working/3D/1037' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(OC)=C1OC(C)=O) `REAL300000086996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086996 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(OC)=C1OC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.2', 'C.3', 'O.2', '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, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 1, 12, 1, 5, 11, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 70, 70, 69, 69, 70, 70, 70, 70, 1, 1, 1, 3, 1, 1, 6, 21, 21, 4, 4, 4, 1, 6, 23, 70, 70, 70, 1, 4, 4, 4, 22, 22, 22] 201 rigid atoms, others: [19, 1, 2, 3, 4, 5, 17, 18, 35, 21, 22, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086996 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])N=C2)=CC(OC)=C1OC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.2', 'C.3', 'O.2', '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, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 1, 12, 1, 5, 11, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 70, 70, 70, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 128, 70, 70, 150, 194, 194, 123, 123, 123, 70, 31, 7, 1, 1, 1, 70, 128, 128, 128, 194, 194, 194] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 584 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086996 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086996 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086996/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086996 Building REAL300000086997 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086997' /scratch/stefan/7769667/working/building/REAL300000086997 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086997 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086997/0 /scratch/stefan/7769667/working/building/REAL300000086997 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1038) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1038 `/scratch/stefan/7769667/working/3D/1038' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21) `REAL300000086997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086997 none CCCN1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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: [5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 1, 1, 1, 1, 1, 1, 1, 7, 39, 39, 38, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 4, 4, 7, 39, 39, 39, 1, 1, 1, 1] 67 rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 36, 38, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086997 none CCCN1C(=O)C(=NNC2=CC=C(C(=O)[O-])N=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', '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: [5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 39, 39, 38, 39, 39, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 67, 67, 67, 67, 67, 67, 67, 13, 1, 1, 1, 39, 39, 39, 39] 67 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086997 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086997 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086997/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086997 Building REAL300000086998 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086998' /scratch/stefan/7769667/working/building/REAL300000086998 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086998 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086998/0 /scratch/stefan/7769667/working/building/REAL300000086998 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1039) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1039 `/scratch/stefan/7769667/working/3D/1039' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3Cl)O2)C=N1) `REAL300000086998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086998 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3Cl)O2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'Cl', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 10, 47, 47, 81, 81, 81, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 1, 1, 1, 1, 10, 47, 82, 81, 201, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27, 28, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086998 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3Cl)O2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'Cl', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 98, 37, 37, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 201, 201, 201, 201, 98, 37, 10, 10, 1, 1, 1, 201] 201 rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 407 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086998 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3Cl)O2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'Cl', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 82, 82, 33, 7, 7, 1, 1, 1, 1, 1, 1, 10, 10, 9, 10, 10, 10, 10, 10, 10, 1, 82, 82, 82, 81, 32, 7, 1, 1, 10, 10, 10, 82] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 167 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086998 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086998 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086998/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086998 Building REAL300000086999 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000086999' /scratch/stefan/7769667/working/building/REAL300000086999 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000086999 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000086999/0 /scratch/stefan/7769667/working/building/REAL300000086999 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1040) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1040 `/scratch/stefan/7769667/working/3D/1040' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])N=C3)O2)C([N+](=O)[O-])=C1) `REAL300000086999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000086999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000086999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086999 none COC1=CC=C(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])N=C3)O2)C([N+](=O)[O-])=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', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', '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, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 12, 1, 8, 11, 11, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 3, 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: [2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 18, 18, 71, 201, 201, 201, 201, 201, 201, 201, 201, 5, 1, 1, 2, 2, 1, 3, 3, 3, 1, 1, 5, 5, 18, 71, 201, 201, 201, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 40, 23, 24, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 368 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086999 none COC1=CC=C(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])N=C3)O2)C([N+](=O)[O-])=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', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', '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, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 12, 1, 8, 11, 11, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 3, 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: [166, 132, 132, 201, 201, 132, 132, 132, 132, 66, 66, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 132, 201, 201, 201, 201, 201, 166, 166, 166, 201, 201, 132, 132, 65, 13, 1, 1, 1, 201] 201 rigid atoms, others: [37, 38, 39, 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, 33, 34, 35, 36, 40]) total number of confs: 571 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000086999 none COC1=CC=C(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])N=C3)O2)C([N+](=O)[O-])=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', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', '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, 8, 1, 1, 1, 1, 1, 11, 11, 8, 1, 12, 1, 8, 11, 11, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 3, 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: [7, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 37, 132, 132, 131, 131, 132, 132, 132, 132, 1, 5, 5, 5, 5, 5, 7, 7, 7, 5, 5, 1, 1, 8, 37, 132, 132, 132, 5] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 34, 22, 33] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000086999 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000086999 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000086999/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000086999 Building REAL300000087000 mkdir: created directory `/scratch/stefan/7769667/working/building/REAL300000087000' /scratch/stefan/7769667/working/building/REAL300000087000 /scratch/stefan/7769667/working /scratch/stefan/7769667 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000087000 mkdir: created directory `0' /scratch/stefan/7769667/working/building/REAL300000087000/0 /scratch/stefan/7769667/working/building/REAL300000087000 /scratch/stefan/7769667/working /scratch/stefan/7769667 Protomer 0 (index: 1041) Found valid previously generated 3D confromation in /scratch/stefan/7769667/working/3D/1041 `/scratch/stefan/7769667/working/3D/1041' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(Cl)C(Cl)=C3)O2)C=N1) `REAL300000087000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000087000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769667/working/building/REAL300000087000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000087000 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(Cl)C(Cl)=C3)O2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 10, 49, 49, 89, 89, 89, 89, 201, 201, 201, 201, 201, 201, 201, 89, 1, 1, 1, 1, 10, 49, 90, 89, 201, 201, 201, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000087000 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(Cl)C(Cl)=C3)O2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 113, 44, 44, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 113, 44, 12, 12, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 439 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000087000 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(Cl)C(Cl)=C3)O2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 12, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 90, 34, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 3, 12, 12, 13, 12, 1, 90, 90, 90, 89, 33, 6, 1, 1, 12, 12, 12, 90] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769667/working/building/REAL300000087000 /scratch/stefan/7769667/working /scratch/stefan/7769667 Finished preparing REAL300000087000 Recording results /scratch/stefan/7769667/working /scratch/stefan/7769667 Appending to /scratch/stefan/7769667/finished/xaaaadi.* 0: /scratch/stefan/7769667/working/building/REAL300000087000/0.* Removing working files in /scratch/stefan/7769667/working/building/REAL300000087000 /scratch/stefan/7769667 Compressing combined databse files /scratch/stefan/7769667/finished/xaaaadi.db2.gz /scratch/stefan/7769667/finished/xaaaadi.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7769667/finished) ======================================================= Finalizing... removed `/scratch/stefan/7769667/working/3D/1042' removed directory: `/scratch/stefan/7769667/working/3D' `/scratch/stefan/7769667/working/protonate' -> `/scratch/stefan/7769667/archive' `/scratch/stefan/7769667/working/input-smiles.ism' -> `/scratch/stefan/7769667/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7769667/working/building' rmdir: removing directory, `/scratch/stefan/7769667/working' ls: No match. ls: No match.